Hi, These are the commands used to call variants using samtools-0.1.19:
samtools mpileup -ABugf ref.fa -l bed -d 1000000 bam | bcftools view -vcg - | vcfutils.pl varFilter -D 1000000 > out.vcf vcfutils.pl varFilter -Q 40 -d 10 out.vcf | awk '$6>=40' > fin.vcf Hope this might help to some extent. On 04/11/14 20:52, Thomas W. Blackwell wrote: > > As with the earlier question, we are all puzzling what could possibly > have introduced N's into the sequence reads. No details of upstream > processing steps are given, so no one has any ideas to contribute. > Simplified command lines and software version numbers are always helpful. > > - tom blackwell - > > On Tue, 4 Nov 2014, Arumilli, Meharji wrote: > >> Hi, >> >> >> I have performed variant calling with samtools. For, some reason some >> of the variants have N in ALT column as shown below: >> >> Chromosome Position SNPid Reference Alternate >> QUAL MQ DP >> chr21 29989187 . A AN 96.50 60 46 >> >> This is a homozygous mutation supported by 46 reads with MQ of 60. >> >> Checked the bam file for this position using mpileup >> >> samtools mpileup -AB -f ref.fa -r chr21:29989186-29989188 input.bam >> >> The output is >> >> chr21 29989187 A 49 >> ....,,,,..,,,,+1n,,...,,,,..,,,,,...,,,...,..,,.,.,^]. >> 7BF<<FFFB7FF<0FIFIIIFBFIIBFFF<IIIFFB<IIFII7BIBIBB >> >> Is this a bug in the code that it is called as "AN" insertion. How >> should i infer this mutation. >> >> Any comments from the users of this community are highly valuable. >> >> >> Br >> Mehar >> >> ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
