Chromosome Maps

It can happen that a BAM file is the result of an alignment using identical reference sequences, but different chromosome name (this is the case, for example, of the samples from Broad that are included in Pf3K, which ise a different name for the MITO sequence).

To obviate this problem, we name a chromosome naming scheme for each BAM file. We specify a master chromosome naming scheme table (a tab-separated text file, with one line for each reference chromosome) that maps chromosome names in the default reference (Sanger V3) against names used in specific schemes, as in:

default	Broad
Pf3D7_01_v3	Pf3D7_01_v3
Pf3D7_02_v3	Pf3D7_02_v3
Pf3D7_03_v3	Pf3D7_03_v3
Pf3D7_04_v3	Pf3D7_04_v3
Pf3D7_05_v3	Pf3D7_05_v3
Pf3D7_06_v3	Pf3D7_06_v3
Pf3D7_07_v3	Pf3D7_07_v3
Pf3D7_08_v3	Pf3D7_08_v3
Pf3D7_09_v3	Pf3D7_09_v3
Pf3D7_10_v3	Pf3D7_10_v3
Pf3D7_11_v3	Pf3D7_11_v3
Pf3D7_12_v3	Pf3D7_12_v3
Pf3D7_13_v3	Pf3D7_13_v3
Pf3D7_14_v3	Pf3D7_14_v3
M76611	Pf_M76611
PFC10_API_IRAB	-

The names "default" and "Broad" can then be used as parameters to indicate the naming scheme to be used when reading the BAM file, e.g. in the sample/BAM list file.

**NOTE: This is not an ideal solution, but it was the simplest way of moving forward for a large set of samples. We will review the strategy in future. **