Hi,
I am upgrading samtools/bcftools from 1.3.1 to 1.5 and I am trying to
understand a difference I spotted.
Using bcftools 1.3.1:
> samtools mpileup -uf ref.fna sample.bam | ./bcftools-1.3.1/bcftools call -c
> --ploidy 1 -
gyrA 284 . A G 77.0075 .
DP=77;VDB=1.03743e-17;SGB=-0.693145;RPB=0.818901;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.5;AC1=1;DP4=7,30,32,8;MQ=20;FQ=79.9725;PV4=7.52472e-08,1,1,0.169748
GT:PL 0:107,127
Using bcftools 1.5:
> samtools mpileup -uf ref.fna sample.bam | bcftools call -c --ploidy 1 -
gyrA 284 . A . 49.9963 .
DP=77;VDB=1.03743e-17;SGB=-0.693145;RPB=0.818901;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.5;AC1=0;DP4=7,30,32,8;MQ=20;FQ=-999;PV4=7.52472e-08,1,1,0.169748
GT:PL 0:107
in both cases samtools was version 1.5
I just wondered what has changed in bcftools for it to call the variant in
version 1.3.1 but not in 1.5 ? By the way, the change must have happened
between 1.3.1 and 1.4 as 1.4 gives the same result as 1.5 above)
Looking at the release notes for 1.4, is this related to "Improved calculation
of the QUAL score particularly for REF sites"?
Thanks for any help
Adam
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