Entering edit mode
4.5 years ago
evelyn
▴
230
Hello,
I used bwa
for alignment and I am using gvcf
for calling variants with this code:
bcftools mpileup -Ov --gvcf 5 -f ref.fa example.sorted.bam | bcftools call -m --gvcf 5 -o example.vcf
I want to keep the homozygous reference calls to distinguish them from any missing calls. I am only interested in SNP variants so after getting the gvcf, I used:
bcftools view --exclude-types indels,mnps,bnd,other example.vcf -o example_1.vcf
I want to use this file for some downstream analysis by merging it with other similar gvcf files. But I noticed that in example.vcf
, there are some positions not called at all which have minimum read depth of 5
as I specified in mpileup
and call
steps. I am pasting some lines from example.vcf:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample.sorted.bam
ch01 195 . G . 29.5864 . DP=1;MQ0F=0;AN=0;DP4=0,0,0,0;MQ=. GT:DP ./.:0
ch01 196 . T . 29.5864 . DP=1;MQ0F=0;AN=0;DP4=0,0,0,0;MQ=. GT:DP ./.:0
ch01 198 . A . 29.5864 . DP=1;MQ0F=0;AN=0;DP4=0,0,0,0;MQ=. GT:DP ./.:0
In IGV
, position 197
has enough reads but gvcf file does not include it. I am not sure why? Thank you for your help!