mpileup and homozygous snps

[grievous]

Hi all,

I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

whole command (samtools-0.1.16):
samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

2. output of bcftools (looks heterozygous to me):
chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

Can anyone tell me the reason for this behaviour?
Thank you.

[idyll_ty]

Have you solved this problem? I also have this problem, and I'm very interested in the result.

Hi all,

I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

whole command (samtools-0.1.16):
samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

2. output of bcftools (looks heterozygous to me):
chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

Can anyone tell me the reason for this behaviour?
Thank you.

[biomichael]

This is surely a heterozygos SNP site from A to G

[maivantan]

2. output of bcftools (looks heterozygous to me):
chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

I think this is heterozygous SNP, you can see this values 0/1:99

[swbarnes2]

Strange. One suggestion...try

samtools mpileup -Buf my.fa my.bam | bcftools view -vcg

The -B turns off BAQ recalculation..I've gotten strange results when it was on, which were repaired by turning it off.

[Jeremy]

You could try a different SNP calling program like freebayes or gatk.