Hi Petr, Thanks for your answer. I tried your suggestions but obtain the same result: an empty VCF file containing only the header. I suspect that something is going wrong with mpileup or with my version of bcftools. Creating a VCF out of my BCF using samtools view, I confirm that my VCF just looks completely normal. I also confirm that I am using versions 1.3.1 and that samtools, bcftools and htslib are all in my PATH.
Please let me know if you have any other suggestions. Antoine > On 05 May 2016, at 09:47, Petr Danecek <p...@sanger.ac.uk> wrote: > > Hi Antoine, > > the usage seems alright. An empty output can be produced when there are > no high confidence calls, try to run without the -v option to get also > non-variant sites on the output. > > Then you can also try "bcftools call -mv". If there is still no output, > try with bigger value of -P, e.g. "bcftools call -mv -P0.01". > > Petr > > On Wed, 2016-05-04 at 12:22 -0400, Antoine Paccard wrote: >> 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 >> Samtools-help@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/samtools-help > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ 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 Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
