Short Variants calling error when using bcftools mpileup

Question

[mike229lin]

Hello,

I want to call gvcf with bcftools mpileup containing variant site and reference homologous site blocks The command line shows below

nohup sh -c "bcftools mpileup -C50 -q25 -g 4 -t DP -f reference.fa sample.bam | bcftools call -c | vcfutils.pl varFilter -d4 -D28 > output.g.vcf" &

I also want to filtrate the variant site out which is 2 times of and one third of the average coverage of each sample. However, it only printed the header out and didn't show any variant site or non variant blocks in my output. How should I edit my command line to manipulate vcf files I want?

Thanks.

[finswimmer]

Hello mike229lin,

you should first check the output after bcftools call -c, if it contains what you expected before starting filtering. Having the header but no variants in the final output sounds like there are nor variants that fulfill the criteria.

Furthermore I wonder if this is correct:

-t DP

The manual says:

-t, --targets REG[,...] similar to -r but streams rather than index-jumps
-r, --regions REG[,...] comma separated list of regions in which pileup is generated

fin swimmer