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r377: increased unpaired penalty from 9 to 17 

This leads to more aggressive pairing - more properly paired reads. I have
found a few cases where, for example, read1 is umambiguously mapped to chr20
while its 100bp mate has a perfect match to another chr but has 3 mismatches
and 1 deletion when it is paired with read1 on chr20. With longer reads, it
seems that the chr20 hit is correct, although it is not obvious how this
happened in evolution.
This commit is contained in:
Heng Li 2013-04-17 16:50:20 -04:00
parent 499cf4c00d
commit 2087dc162f
3 changed files with 4 additions and 4 deletions
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4
bwa.1
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@ -1,4 +1,4 @@
.TH bwa 1 "15 March 2013" "bwa-0.7.3a" "Bioinformatics tools"
.TH bwa 1 "15 March 2013" "bwa-0.7.4" "Bioinformatics tools"
.SH NAME
.PP
bwa - Burrows-Wheeler Alignment Tool
@ -220,7 +220,7 @@ deducted. [5]
Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as
.RI scoreRead1+scoreRead2- INT
and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these
two scores to determine whether we should force pairing. [9]
two scores to determine whether we should force pairing. [17]
.TP
.B -p
Assume the first input query file is interleaved paired-end FASTA/Q. See the command description for details.

2
bwamem.c
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@ -46,7 +46,7 @@ mem_opt_t *mem_opt_init()
o->a = 1; o->b = 4; o->q = 6; o->r = 1; o->w = 100;
o->T = 30;
o->zdrop = 100;
o->pen_unpaired = 9;
o->pen_unpaired = 17;
o->pen_clip = 5;
o->min_seed_len = 19;
o->split_width = 10;

2
main.c
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@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3-r376-beta"
#define PACKAGE_VERSION "0.7.3-r377-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);