I am trying to produce a vcf file using bcftools call but it produces an empty vcf file containing only the header. In short, here is what I do:
- Alignment with BWA
- With samtools, make sorted.bam files
- With samtools, index the sorted.bam files
- Run samtools mpileup in the following way: samtools mpileup -C 50 -E -t SP -t DP -u -I –f /genome/refgenome.fa -b bam_list.txt > output.bcf
- Run bcftools call: bcftools call -v -c output.bcf > output.vcf
I am using versions 1.3.1 of samtools, bcftools and htslib. I tried reinstalling these programs but it did not change the issue. I also tried with versions 1.2. Same problem. As far as I know, the bcf file seems fine, it contains lots of data and is 20GB.
I tried producing a basic vcf file using bcftools view: bcftools view output.cf > output.vcf and it works. The vcf file seems completely normal.
Could anyone help me with this? Why would bcftools call produce an empty output?