HI everyone,
Solved!
I had to use the -x option in samtools/1.2, (--ignore-overlaps - disable
read-pair overlap detection) so that the read depth values match those produced
with samtools/0.1.19
Dessi
From: Dessislava Mladenova
<[email protected]<mailto:[email protected]>>
Date: Tue, 19 May 2015 06:21:17 +0000
To:
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [Samtools-help] mpileup discrepancy Samtools 0.1.19 and 1.2 for depth
values
Hi everyone
I have used Samtools 0.1.19 and 1.2 versions mpileup to view positions with
mismatches to the reference genome.
However with exactly the same settings the first 4 values in the I16 tag
(reference bases forward, reference bases reverse strand, alt forward,
alternative reverse) do not match between the two versions:
samtools mpileup -g -B -Q 30 -f genome.fa -l my.bed my.bam1 my.bam2 my.bam3 >
my.bcf
bcftools/1.0
Compare:
bcftools view my.vcf | grep 64753439
file generated with Samtools 1.2
chr7 64753439 . A G,<X> 0 .
DP=792;I16=122,200,36,285,15279,812733,11867,477401,6440,128800,6420,128400,2991,47307,93,105;QS=2.57949,3.42051,0;VDB=0;SGB=-104.385;RPB=0;MQB=1;MQSB=1;BQB=0;MQ0F=0
PL 0,37,123,255,247,212 0,55,155,255,233,209 114,0,21,150,159,190
128,0,77,213,255,240 113,0,39,173,214,203 112,0,16,197,255,215
file generated with Samtools 0.1.19
chr7 64753439 . A G,X 0 .
DP=792;I16=119,299,38,321,15322,563512,11935,397431,8360,167200,7180,143600,3909,60917,133,147;QS=0.537967,0.462033,0.000000,0.000000;VDB=0;RPB=23.5676
PL 0,113,162,255,255,239 0,106,176,255,255,226
113,0,40,161,197,206 131,0,102,242,255,255 125,0,79,212,255,245
122,0,28,237,255,231
Can someone help to identify the reason for this discrepancy?
Note that the values from Samtools 0.1.19 match more closely the values seen
in IGV, so I would like to use them. However, it seems the VDB value I need for
filtering may be broken in the Samtools 0.1.19 version? All VDB values are in
the range 0 to 0.5 for my data.
Thank you very much!
Dessi
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