Hello, 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:
1. Alignment with BWA 2. With samtools, make sorted.bam files 3. With samtools, index the sorted.bam files 4. 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 5. 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? Thanks ------------------------------------------------------------------------------ Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
