Hi All,
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
Compare
bcftools/1.0
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?
Thank you very much!
Dessi