nurmians/POPBAM-multiregiontree

POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments

POPBAM - multiregiontree

This fork of POPBAM fixes segmentation fault at treeData::join_tree and enables summming up multiple regions' diff matrices before calculating distance matrix for the whole tree.

Example @RG data with required "PO"-field for merged bam file

bwa mem -t 14 -H header_sq.txt -R "@RG\tSM:SRR8177528\tID:SRR8177528.dm6.PE\tLB:0\tPL:ILLUMINA\tPU:SRR8177528_1\tPO:SRR8177528" ...

Example @SQ header for the fruit fly

@SQ SN:chr2L LN:23513712 AS:dm6 @SQ SN:chr2R LN:25286936 AS:dm6 @SQ SN:chr3L LN:28110227 AS:dm6 @SQ SN:chr3R LN:32079331 AS:dm6 @SQ SN:chr4 LN:1348131 AS:dm6 @SQ SN:chrM LN:19524 AS:dm6 @SQ SN:chrX LN:23542271 AS:dm6 @SQ SN:chrY LN:3667352 AS:dm6