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