The new command is `bcftools call`, sorry for the confusion. petr
On Wed, 2014-10-29 at 13:00 +0000, the all-new magic tortoise z wrote: > i'm struggling to include MQ in my version 1.1 mpileup vcf output. > this used to be easy with the samtools version that i used previously. > maybe i'm missing something simple. > > my whole command looks a little like this, and doesn't give MQs: > > samtools mpileup -g -I -f b37.fa bam1.bam bam2.bam -l bed.bed | bcftools view > -O v -o out.vcf > > including "-s" means put MQ in output, but only if you don't use bcf/vcf, so > that's no good, right? ...and indeed i get the same vcf with no MQs. > > -t could be the answer, but i haven't managed to use it correctly yet. > i've tried including "-t MQ" and get this error: > Could not parse tag "MQ" in "MQ" > > similarly, i tried "-t INFO" (as i'm aiming to get it into the info field of > the vcf ... clutching at straws) and got the same error. > > any way to avoid these probs and make a vcf with MQ values? > > thanks > ------------------------------------------------------------------------------ > _______________________________________________ > 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. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
