gatkcmds-gen.sh

#!/bin/bash
windows="/work/LAS/mhufford-lab/arnstrm/NAM/rnaseq/00_B73index/windows-large.bed"
ref="/work/LAS/mhufford-lab/arnstrm/NAM/rnaseq/00_B73index/B73.fasta"
while read line; do
out=$(echo $line |sed 's/:/_/g')
echo "java -Xmx75g -Djava.io.tmpdir=\$TMPDIR  -jar /opt/rit/spack-app/linux-rhel7-x86_64/gcc-4.8.5/gatk-4.0.4.0-2rrbjyxlafz4nrrskjn7rtykbsq3nh4f/bin/gatk-package-4.0.4.0-local.jar HaplotypeCaller --reference $ref --dont-use-soft-clipped-bases true -I B73_16DAP_embryo_MN01101_split.bam -I B73_16DAP_embryo_MN01102_split.bam -I B73_16DAP_endosperm_MN01091_split.bam -I B73_16DAP_endosperm_MN01092_split.bam -I B73_8DAS_root_MN01011_split.bam -I B73_8DAS_root_MN01012_split.bam -I B73_8DAS_shoot_MN01021_split.bam -I B73_8DAS_shoot_MN01022_split.bam -I B73Ab10_16DAP_embryo_MN02101_split.bam -I B73Ab10_16DAP_embryo_MN02102_split.bam -I B73Ab10_16DAP_endosperm_MN02091_split.bam -I B73Ab10_16DAP_endosperm_MN02092_split.bam -I B73Ab10_8DAS_root_MN02011_split.bam -I B73Ab10_8DAS_root_MN02012_split.bam -I B73Ab10_8DAS_shoot_MN02021_split.bam -I B73Ab10_8DAS_shoot_MN02022_split.bam -I B73Ab10_R1_anther_MN02081_split.bam -I B73Ab10_R1_anther_MN02082_split.bam -I B73Ab10_V11_base_MN02031_split.bam -I B73Ab10_V11_base_MN02032_split.bam -I B73Ab10_V11_middle_MN02041_split.bam -I B73Ab10_V11_middle_MN02042_split.bam -I B73Ab10_V11_tip_MN02051_split.bam -I B73Ab10_V11_tip_MN02052_split.bam -I B73Ab10_V18_ear_MN02071_split.bam -I B73Ab10_V18_ear_MN02072_split.bam -I B73Ab10_V18_tassel_MN02061_split.bam -I B73Ab10_V18_tassel_MN02062_split.bam -I B73_R1_anther_MN01081_split.bam -I B73_R1_anther_MN01082_split.bam -I B73_R1_anther_MNA1081_split.bam -I B73_V11_base_MN01031_split.bam -I B73_V11_base_MN01032_split.bam -I B73_V11_middle_MN01041_split.bam -I B73_V11_middle_MN01042_split.bam -I B73_V11_middle_MN01043_split.bam -I B73_V11_tip_MN01051_split.bam -I B73_V11_tip_MN01052_split.bam -I B73_V18_ear_MN01071_split.bam -I B73_V18_ear_MN01072_split.bam -I B73_V18_tassel_MN01061_split.bam -I B73_V18_tassel_MN01062_split.bam -I B97_16DAP_embryo_MN03101_split.bam -I B97_16DAP_embryo_MN03102_split.bam -I B97_16DAP_endosperm_MN03091_split.bam -I B97_16DAP_endosperm_MN03092_split.bam -I B97_8DAS_root_MN03011_split.bam -I B97_8DAS_root_MN03012_split.bam -I B97_8DAS_shoot_MN03021_split.bam -I B97_8DAS_shoot_MN03022_split.bam -I B97_R1_anther_MN03081_split.bam -I B97_R1_anther_MN03082_split.bam -I B97_V11_base_MN03031_split.bam -I B97_V11_base_MN03032_split.bam -I B97_V11_middle_MN03041_split.bam -I B97_V11_middle_MN03042_split.bam -I B97_V11_tip_MN03051_split.bam -I B97_V11_tip_MN03052_split.bam -I B97_V11_tip_MN03053_split.bam -I B97_V18_ear_MN03071_split.bam -I B97_V18_ear_MN03072_split.bam -I B97_V18_tassel_MN03061_split.bam -I B97_V18_tassel_MN03062_split.bam -I CML103_16DAP_embryo_MN04101_split.bam -I CML103_16DAP_embryo_MN04102_split.bam -I CML103_16DAP_endosperm_MN04091_split.bam -I CML103_16DAP_endosperm_MN04092_split.bam -I CML103_8DAS_root_MN04011_split.bam -I CML103_8DAS_root_MN04012_split.bam -I CML103_8DAS_shoot_MN04021_split.bam -I CML103_8DAS_shoot_MN04022_split.bam -I CML103_R1_anther_MN04081_split.bam -I CML103_R1_anther_MN04082_split.bam -I CML103_V11_base_MN04031_split.bam -I CML103_V11_base_MN04032_split.bam -I CML103_V11_middle_MN04041_split.bam -I CML103_V11_middle_MN04042_split.bam -I CML103_V11_tip_MN04051_split.bam -I CML103_V11_tip_MN04052_split.bam -I CML103_V18_ear_MN04071_split.bam -I CML103_V18_ear_MN04072_split.bam -I CML103_V18_tassel_MN04061_split.bam -I CML227_8DAS_root_MN05011_split.bam -I CML227_8DAS_root_MN05012_split.bam -I CML227_8DAS_shoot_MN05021_split.bam -I CML227_8DAS_shoot_MN05022_split.bam -I CML227_R1_anther_MN05081_split.bam -I CML227_R1_anther_MN05082_split.bam -I CML227_V11_base_MN05031_split.bam -I CML227_V11_base_MN05032_split.bam -I CML227_V11_middle_MN05041_split.bam -I CML227_V11_middle_MN05042_split.bam -I CML227_V11_tip_MN05051_split.bam -I CML227_V11_tip_MN05052_split.bam -I CML227_V18_ear_MN05071_split.bam -I CML227_V18_ear_MN05072_split.bam -I CML227_V18_tassel_MN05061_split.bam -I CML227_V18_tassel_MN05062_split.bam -I CML228_8DAS_root_MN06011_split.bam -I CML228_8DAS_root_MN06012_split.bam -I CML228_8DAS_shoot_MN06021_split.bam -I CML228_8DAS_shoot_MN06022_split.bam -I CML228_R1_anther_MN06081_split.bam -I CML228_R1_anther_MN06082_split.bam -I CML228_V11_base_MN06031_split.bam -I CML228_V11_base_MN06032_split.bam -I CML228_V11_middle_MN06041_split.bam -I CML228_V11_middle_MN06042_split.bam -I CML228_V11_tip_MN06051_split.bam -I CML228_V11_tip_MN06052_split.bam -I CML228_V18_ear_MN06071_split.bam -I CML228_V18_ear_MN06072_split.bam -I CML228_V18_tassel_MN06061_split.bam -I CML228_V18_tassel_MN06062_split.bam -I CML247_8DAS_root_MN07011_split.bam -I CML247_8DAS_root_MN07012_split.bam -I CML247_8DAS_shoot_MN07021_split.bam -I CML247_8DAS_shoot_MN07022_split.bam -I CML247_R1_anther_MN07081_split.bam -I CML247_R1_anther_MN07082_split.bam -I CML247_V11_base_MN07031_split.bam -I CML247_V11_base_MN07033_split.bam -I CML247_V11_middle_MN07042_split.bam -I CML247_V11_middle_MN07043_split.bam -I CML247_V11_tip_MN07051_split.bam -I CML247_V11_tip_MN07053_split.bam -I CML247_V18_ear_MN07071_split.bam -I CML247_V18_ear_MN07072_split.bam -I CML247_V18_tassel_MN07061_split.bam -I CML247_V18_tassel_MN07062_split.bam -I CML322_16DAP_embryo_MN08101_split.bam -I CML322_16DAP_embryo_MN08102_split.bam -I CML322_16DAP_endosperm_MN08091_split.bam -I CML322_16DAP_endosperm_MN08092_split.bam -I CML322_8DAS_root_MN08011_split.bam -I CML322_8DAS_root_MN08012_split.bam -I CML322_8DAS_shoot_MN08021_split.bam -I CML322_8DAS_shoot_MN08022_split.bam -I CML322_R1_anther_MN08081_split.bam -I CML322_R1_anther_MN08082_split.bam -I CML322_V11_base_MN08031_split.bam -I CML322_V11_base_MN08032_split.bam -I CML322_V11_middle_MN08041_split.bam -I CML322_V11_middle_MN08042_split.bam -I CML322_V11_tip_MN08051_split.bam -I CML322_V11_tip_MN08052_split.bam -I CML322_V11_tip_MN08053_split.bam -I CML322_V18_ear_MN08071_split.bam -I CML322_V18_ear_MN08072_split.bam -I CML322_V18_tassel_MN08061_split.bam -I CML322_V18_tassel_MN08062_split.bam -I CML333_8DAS_root_MN09011_split.bam -I CML333_8DAS_root_MN09012_split.bam -I CML333_8DAS_shoot_MN09021_split.bam -I CML333_8DAS_shoot_MN09022_split.bam -I CML333_R1_anther_MN09081_split.bam -I CML333_R1_anther_MN09082_split.bam -I CML333_V11_base_MN09031_split.bam -I CML333_V11_base_MN09032_split.bam -I CML333_V11_middle_MN09041_split.bam -I CML333_V11_middle_MN09042_split.bam -I CML333_V11_tip_MN09051_split.bam -I CML333_V11_tip_MN09052_split.bam -I CML333_V18_ear_MN09071_split.bam -I CML333_V18_ear_MN09072_split.bam -I CML333_V18_tassel_MN09061_split.bam -I CML333_V18_tassel_MN09062_split.bam -I CML52_8DAS_root_MN10011_split.bam -I CML52_8DAS_root_MN10012_split.bam -I CML52_8DAS_shoot_MN10021_split.bam -I CML52_8DAS_shoot_MN10022_split.bam -I CML52_R1_anther_MN10081_split.bam -I CML52_R1_anther_MN10082_split.bam -I CML52_V11_base_MN10031_split.bam -I CML52_V11_base_MN10032_split.bam -I CML52_V11_middle_MN10041_split.bam -I CML52_V11_middle_MN10042_split.bam -I CML52_V11_tip_MN10051_split.bam -I CML52_V11_tip_MN10052_split.bam -I CML52_V18_ear_MN10071_split.bam -I CML52_V18_ear_MN10072_split.bam -I CML52_V18_tassel_MN10061_split.bam -I CML52_V18_tassel_MN10062_split.bam -I CML69_16DAP_embryo_MN11101_split.bam -I CML69_16DAP_embryo_MN11102_split.bam -I CML69_16DAP_endosperm_MN11091_split.bam -I CML69_16DAP_endosperm_MN11092_split.bam -I CML69_8DAS_root_MN11011_split.bam -I CML69_8DAS_root_MN11012_split.bam -I CML69_8DAS_shoot_MN11021_split.bam -I CML69_8DAS_shoot_MN11022_split.bam -I CML69_R1_anther_MN11081_split.bam -I CML69_R1_anther_MN11082_split.bam -I CML69_V11_base_MN11031_split.bam -I CML69_V11_base_MN11032_split.bam -I CML69_V11_middle_MN11041_split.bam -I CML69_V11_middle_MN11042_split.bam -I CML69_V11_tip_MN11051_split.bam -I CML69_V11_tip_MN11052_split.bam -I CML69_V18_ear_MN11071_split.bam -I CML69_V18_ear_MN11072_split.bam -I CML69_V18_tassel_MN11061_split.bam -I CML69_V18_tassel_MN11062_split.bam -I HP301_16DAP_embryo_MN12101_split.bam -I HP301_16DAP_embryo_MN12102_split.bam -I HP301_16DAP_endosperm_MN12091_split.bam -I HP301_16DAP_endosperm_MN12092_split.bam -I HP301_16DAP_endosperm_MN12093_split.bam -I HP301_8DAS_root_MN12011_split.bam -I HP301_8DAS_root_MN12012_split.bam -I HP301_8DAS_shoot_MN12021_split.bam -I HP301_8DAS_shoot_MN12022_split.bam -I HP301_R1_anther_MN12081_split.bam -I HP301_R1_anther_MN12082_split.bam -I HP301_V11_base_MN12031_split.bam -I HP301_V11_base_MN12032_split.bam -I HP301_V11_middle_MN12041_split.bam -I HP301_V11_middle_MN12042_split.bam -I HP301_V11_tip_MN12051_split.bam -I HP301_V11_tip_MN12052_split.bam -I HP301_V18_ear_MN12071_split.bam -I HP301_V18_ear_MN12072_split.bam -I HP301_V18_tassel_MN12061_split.bam -I HP301_V18_tassel_MN12062_split.bam -I IL14H_16DAP_embryo_MN13102_split.bam -I IL14H_16DAP_endosperm_MN13091_split.bam -I IL14H_16DAP_endosperm_MN13092_split.bam -I IL14H_8DAS_root_MN13011_split.bam -I IL14H_8DAS_root_MN13012_split.bam -I IL14H_8DAS_shoot_MN13021_split.bam -I IL14H_8DAS_shoot_MN13022_split.bam -I IL14H_R1_anther_MN13081_split.bam -I IL14H_R1_anther_MN13082_split.bam -I IL14H_V11_base_MN13031_split.bam -I IL14H_V11_base_MN13032_split.bam -I IL14H_V11_middle_MN13041_split.bam -I IL14H_V11_middle_MN13042_split.bam -I IL14H_V11_tip_MN13051_split.bam -I IL14H_V11_tip_MN13052_split.bam -I IL14H_V18_ear_MN13071_split.bam -I IL14H_V18_ear_MN13072_split.bam -I IL14H_V18_tassel_MN13061_split.bam -I IL14H_V18_tassel_MN13062_split.bam -I KI11_16DAP_embryo_MN14102_split.bam -I KI11_16DAP_endosperm_MN14092_split.bam -I KI11_8DAS_root_MN14011_split.bam -I KI11_8DAS_root_MN14012_split.bam -I KI11_8DAS_shoot_MN14021_split.bam -I KI11_8DAS_shoot_MN14022_split.bam -I KI11_R1_anther_MN14081_split.bam -I KI11_R1_anther_MN14082_split.bam -I KI11_V11_base_MN14031_split.bam -I KI11_V11_base_MN14032_split.bam -I KI11_V11_middle_MN14041_split.bam -I KI11_V11_middle_MN14042_split.bam -I KI11_V11_tip_MN14051_split.bam -I KI11_V11_tip_MN14052_split.bam -I KI11_V18_ear_MN14071_split.bam -I KI11_V18_ear_MN14072_split.bam -I KI11_V18_tassel_MN14061_split.bam -I KI11_V18_tassel_MN14062_split.bam -I Ki3_16DAP_embryo_MN15101_split.bam -I Ki3_8DAS_root_MN15011_split.bam -I Ki3_8DAS_root_MN15012_split.bam -I Ki3_8DAS_root_MN15013_split.bam -I Ki3_8DAS_shoot_MN15021_split.bam -I Ki3_8DAS_shoot_MN15022_split.bam -I Ki3_R1_anther_MN15081_split.bam -I Ki3_R1_anther_MN15082_split.bam -I Ki3_V11_base_MN15031_split.bam -I Ki3_V11_base_MN15032_split.bam -I Ki3_V11_middle_MN15041_split.bam -I Ki3_V11_middle_MN15042_split.bam -I Ki3_V11_tip_MN15051_split.bam -I Ki3_V11_tip_MN15052_split.bam -I Ki3_V18_ear_MN15071_split.bam -I Ki3_V18_ear_MN15072_split.bam -I Ki3_V18_tassel_MN15061_split.bam -I Ki3_V18_tassel_MN15062_split.bam -I Ky21_16DAP_embryo_MN16101_split.bam -I Ky21_16DAP_embryo_MN16102_split.bam -I Ky21_16DAP_endosperm_MN16091_split.bam -I Ky21_16DAP_endosperm_MN16092_split.bam -I Ky21_8DAS_root_MN16011_split.bam -I Ky21_8DAS_root_MN16012_split.bam -I Ky21_8DAS_shoot_MN16021_split.bam -I Ky21_8DAS_shoot_MN16022_split.bam -I Ky21_R1_anther_MN16081_split.bam -I Ky21_R1_anther_MN16082_split.bam -I Ky21_V11_base_MN16031_split.bam -I Ky21_V11_base_MN16033_split.bam -I Ky21_V11_middle_MN16041_split.bam -I Ky21_V11_middle_MN16042_split.bam -I Ky21_V11_middle_MN16043_split.bam -I Ky21_V11_tip_MN16051_split.bam -I Ky21_V11_tip_MN16053_split.bam -I Ky21_V18_ear_MN16071_split.bam -I Ky21_V18_ear_MN16072_split.bam -I Ky21_V18_tassel_MN16061_split.bam -I Ky21_V18_tassel_MN16062_split.bam -I M162W_16DAP_embryo_MN17102_split.bam -I M162W_16DAP_endosperm_MN17091_split.bam -I M162W_16DAP_endosperm_MN17092_split.bam -I M162W_8DAS_root_MN17011_split.bam -I M162W_8DAS_root_MN17012_split.bam -I M162W_8DAS_shoot_MN17021_split.bam -I M162W_8DAS_shoot_MN17022_split.bam -I M162W_R1_anther_MN17081_split.bam -I M162W_R1_anther_MN17082_split.bam -I M162W_V11_base_MN17032_split.bam -I M162W_V11_base_MN17033_split.bam -I M162W_V11_middle_MN17042_split.bam -I M162W_V11_middle_MN17043_split.bam -I M162W_V11_tip_MN17052_split.bam -I M162W_V11_tip_MN17053_split.bam -I M162W_V18_ear_MN17071_split.bam -I M162W_V18_ear_MN17072_split.bam -I M162W_V18_tassel_MN17061_split.bam -I M162W_V18_tassel_MN17062_split.bam -I M37W_16DAP_embryo_MN18101_split.bam -I M37W_16DAP_embryo_MN18102_split.bam -I M37W_16DAP_endosperm_MN18091_split.bam -I M37W_16DAP_endosperm_MN18092_split.bam -I M37W_8DAS_root_MN18011_split.bam -I M37W_8DAS_root_MN18012_split.bam -I M37W_8DAS_shoot_MN18021_split.bam -I M37W_8DAS_shoot_MN18022_split.bam -I M37W_R1_anther_MN18081_split.bam -I M37W_R1_anther_MN18082_split.bam -I M37W_V11_base_MN18031_split.bam -I M37W_V11_base_MN18032_split.bam -I M37W_V11_middle_MN18041_split.bam -I M37W_V11_middle_MN18042_split.bam -I M37W_V11_tip_MN18051_split.bam -I M37W_V11_tip_MN18052_split.bam -I M37W_V18_ear_MN18071_split.bam -I M37W_V18_ear_MN18072_split.bam -I M37W_V18_tassel_MN18061_split.bam -I M37W_V18_tassel_MN18062_split.bam -I Mo18w_16DAP_embryo_MN19101_split.bam -I Mo18w_16DAP_embryo_MN19102_split.bam -I Mo18w_16DAP_endosperm_MN19092_split.bam -I Mo18w_8DAS_root_MN19011_split.bam -I Mo18w_8DAS_root_MN19012_split.bam -I Mo18w_8DAS_shoot_MN19021_split.bam -I Mo18w_8DAS_shoot_MN19022_split.bam -I Mo18w_R1_anther_MN19081_split.bam -I Mo18w_R1_anther_MN19082_split.bam -I Mo18w_V11_base_MN19031_split.bam -I Mo18w_V11_base_MN19032_split.bam -I Mo18w_V11_middle_MN19041_split.bam -I Mo18w_V11_middle_MN19042_split.bam -I Mo18w_V11_tip_MN19051_split.bam -I Mo18w_V11_tip_MN19052_split.bam -I Mo18w_V18_ear_MN19071_split.bam -I Mo18w_V18_ear_MN19072_split.bam -I Mo18w_V18_tassel_MN19061_split.bam -I Mo18w_V18_tassel_MN19062_split.bam -I Ms71_16DAP_embryo_MN20101_split.bam -I Ms71_16DAP_embryo_MN20102_split.bam -I Ms71_16DAP_endosperm_MN20091_split.bam -I Ms71_16DAP_endosperm_MN20092_split.bam -I Ms71_8DAS_root_MN20011_split.bam -I Ms71_8DAS_root_MN20012_split.bam -I Ms71_8DAS_shoot_MN20021_split.bam -I Ms71_8DAS_shoot_MN20022_split.bam -I Ms71_R1_anther_MN20081_split.bam -I Ms71_R1_anther_MN20082_split.bam -I Ms71_V11_base_MN20031_split.bam -I Ms71_V11_base_MN20032_split.bam -I Ms71_V11_middle_MN20041_split.bam -I Ms71_V11_middle_MN20042_split.bam -I Ms71_V11_tip_MN20051_split.bam -I Ms71_V11_tip_MN20052_split.bam -I Ms71_V18_ear_MN20071_split.bam -I Ms71_V18_ear_MN20072_split.bam -I Ms71_V18_tassel_MN20061_split.bam -I Ms71_V18_tassel_MN20062_split.bam -I NC350_16DAP_embryo_MN21101_split.bam -I NC350_16DAP_embryo_MN21102_split.bam -I NC350_8DAS_root_MN21011_split.bam -I NC350_8DAS_root_MN21012_split.bam -I NC350_8DAS_shoot_MN21021_split.bam -I NC350_8DAS_shoot_MN21022_split.bam -I NC350_R1_anther_MN21081_split.bam -I NC350_R1_anther_MN21082_split.bam -I NC350_V11_base_MN21031_split.bam -I NC350_V11_base_MN21032_split.bam -I NC350_V11_base_MN21033_split.bam -I NC350_V11_middle_MN21041_split.bam -I NC350_V11_middle_MN21042_split.bam -I NC350_V11_tip_MN21051_split.bam -I NC350_V11_tip_MN21052_split.bam -I NC350_V18_ear_MN21071_split.bam -I NC350_V18_ear_MN21072_split.bam -I NC350_V18_tassel_MN21061_split.bam -I NC350_V18_tassel_MN21062_split.bam -I NC358_16DAP_embryo_MN22101_split.bam -I NC358_16DAP_embryo_MN22102_split.bam -I NC358_16DAP_endosperm_MN22091_split.bam -I NC358_16DAP_endosperm_MN22092_split.bam -I NC358_8DAS_root_MN22011_split.bam -I NC358_8DAS_root_MN22012_split.bam -I NC358_8DAS_shoot_MN22021_split.bam -I NC358_8DAS_shoot_MN22022_split.bam -I NC358_R1_anther_MN22081_split.bam -I NC358_R1_anther_MN22082_split.bam -I NC358_V11_base_MN22031_split.bam -I NC358_V11_base_MN22032_split.bam -I NC358_V11_middle_MN22041_split.bam -I NC358_V11_middle_MN22042_split.bam -I NC358_V11_tip_MN22051_split.bam -I NC358_V11_tip_MN22052_split.bam -I NC358_V18_ear_MN22071_split.bam -I NC358_V18_ear_MN22073_split.bam -I NC358_V18_tassel_MN22061_split.bam -I NC358_V18_tassel_MN22062_split.bam -I Oh43_16DAP_embryo_MN23101_split.bam -I Oh43_16DAP_embryo_MN23102_split.bam -I Oh43_16DAP_endosperm_MN23091_split.bam -I Oh43_16DAP_endosperm_MN23092_split.bam -I Oh43_8DAS_root_MN23011_split.bam -I Oh43_8DAS_root_MN23012_split.bam -I Oh43_8DAS_root_MN23013_split.bam -I Oh43_8DAS_shoot_MN23021_split.bam -I Oh43_8DAS_shoot_MN23022_split.bam -I Oh43_R1_anther_MN23081_split.bam -I Oh43_R1_anther_MN23082_split.bam -I Oh43_V11_base_MN23031_split.bam -I Oh43_V11_base_MN23032_split.bam -I Oh43_V11_middle_MN23041_split.bam -I Oh43_V11_middle_MN23042_split.bam -I Oh43_V11_tip_MN23051_split.bam -I Oh43_V11_tip_MN23052_split.bam -I Oh43_V18_ear_MN23071_split.bam -I Oh43_V18_ear_MN23072_split.bam -I Oh43_V18_tassel_MN23061_split.bam -I Oh43_V18_tassel_MN23062_split.bam -I Oh7b_16DAP_embryo_MN24101_split.bam -I Oh7b_16DAP_embryo_MN24102_split.bam -I Oh7b_16DAP_endosperm_MN24091_split.bam -I Oh7b_16DAP_endosperm_MN24092_split.bam -I Oh7b_8DAS_root_MN24011_split.bam -I Oh7b_8DAS_root_MN24012_split.bam -I Oh7b_8DAS_shoot_MN24021_split.bam -I Oh7b_8DAS_shoot_MN24022_split.bam -I Oh7b_R1_anther_MN24081_split.bam -I Oh7b_R1_anther_MN24082_split.bam -I Oh7b_V11_base_MN24031_split.bam -I Oh7b_V11_base_MN24032_split.bam -I Oh7b_V11_middle_MN24041_split.bam -I Oh7b_V11_middle_MN24042_split.bam -I Oh7b_V11_tip_MN24051_split.bam -I Oh7b_V11_tip_MN24052_split.bam -I Oh7b_V18_ear_MN24071_split.bam -I Oh7b_V18_ear_MN24072_split.bam -I Oh7b_V18_tassel_MN24061_split.bam -I Oh7b_V18_tassel_MN24062_split.bam -I P39_16DAP_embryo_MN25101_split.bam -I P39_16DAP_embryo_MN25102_split.bam -I P39_16DAP_endosperm_MN25091_split.bam -I P39_16DAP_endosperm_MN25092_split.bam -I P39_8DAS_root_MN25011_split.bam -I P39_8DAS_root_MN25012_split.bam -I P39_8DAS_shoot_MN25021_split.bam -I P39_8DAS_shoot_MN25022_split.bam -I P39_R1_anther_MN25081_split.bam -I P39_R1_anther_MN25082_split.bam -I P39_V11_base_MN25031_split.bam -I P39_V11_base_MN25032_split.bam -I P39_V11_middle_MN25041_split.bam -I P39_V11_middle_MN25042_split.bam -I P39_V11_tip_MN25051_split.bam -I P39_V11_tip_MN25052_split.bam -I P39_V18_ear_MN25071_split.bam -I P39_V18_ear_MN25072_split.bam -I P39_V18_tassel_MN25061_split.bam -I P39_V18_tassel_MN25062_split.bam -I TX303_16DAP_embryo_MN26101_split.bam -I TX303_16DAP_embryo_MN26103_split.bam -I TX303_16DAP_endosperm_MN26091_split.bam -I TX303_16DAP_endosperm_MN26093_split.bam -I TX303_8DAS_root_MN26011_split.bam -I TX303_8DAS_root_MN26012_split.bam -I TX303_8DAS_shoot_MN26021_split.bam -I TX303_8DAS_shoot_MN26022_split.bam -I TX303_R1_anther_MN26081_split.bam -I TX303_R1_anther_MN26082_split.bam -I TX303_V11_base_MN26031_split.bam -I TX303_V11_base_MN26032_split.bam -I TX303_V11_base_MN26033_split.bam -I TX303_V11_middle_MN26041_split.bam -I TX303_V11_middle_MN26042_split.bam -I TX303_V11_middle_MN26043_split.bam -I TX303_V11_tip_MN26051_split.bam -I TX303_V11_tip_MN26052_split.bam -I TX303_V11_tip_MN26053_split.bam -I TX303_V18_ear_MN26071_split.bam -I TX303_V18_ear_MN26072_split.bam -I TX303_V18_tassel_MN26061_split.bam -I TX303_V18_tassel_MN26062_split.bam -I TZI-8_16DAP_embryo_MN27101_split.bam -I TZI-8_16DAP_embryo_MN27102_split.bam -I TZI-8_16DAP_endosperm_MN27091_split.bam -I TZI-8_16DAP_endosperm_MN27092_split.bam -I TZI-8_8DAS_root_MN27011_split.bam -I TZI-8_8DAS_root_MN27012_split.bam -I TZI-8_8DAS_shoot_MN27021_split.bam -I TZI-8_8DAS_shoot_MN27022_split.bam -I TZI-8_R1_anther_MN27081_split.bam -I TZI-8_R1_anther_MN27082_split.bam -I TZI-8_V11_base_MN27031_split.bam -I TZI-8_V11_base_MN27032_split.bam -I TZI-8_V11_middle_MN27041_split.bam -I TZI-8_V11_middle_MN27042_split.bam -I TZI-8_V11_tip_MN27051_split.bam -I TZI-8_V11_tip_MN27052_split.bam -I TZI-8_V18_ear_MN27071_split.bam -I TZI-8_V18_ear_MN27072_split.bam -I TZI-8_V18_tassel_MN27061_split.bam -I TZI-8_V18_tassel_MN27062_split.bam -I UNK_unk_tissue_MN00000_split.bam -L ${line} --output ${out}.vcf"
done<$windows