Dear All, I have performed samtools for variant calling I have found variants in pileup file but not in vcf file. please find below one example for your concern.
chromosome 1082014 G 230 a$,aaAAaaAAAAA,,a,aaaaaAaaaaaaAAaaa.ATaaAaaAaa,aaaAAAaaAtAa.A,,taaaa.AAa,aaAa,,aAaAaataaAaaaaAA,taaaAaaA,,,aaaa,AAAAAatA.a.,aA.taaAa.a,,,,aaa,aaaAAaAaAaaAA...aa,aAA,a,AaaAa,AAAAaA.aaa,aaaaaaAA..,a.t,aaaaa 'A>=<<@AF<<..FFFAFFFAAFAFFFFFC..FFF..AFFC.<A.FCFF8AF?.A.AFFFFF.FF.F7FF)FA)7.FFF.FF.F)FAFFAFFFFF)<FFF..F.FFFFFFFFFA)FF7<FFAF.FF.FF<F7)FFFF))F<..FAFAF7F.<FFAFF7)F.FFFFFABFAFFFFFFFFA..<FF.FFF7.C7FFFF.F8.... parameters: /data/ngs/Programs/samtools-0.1.18/samtools mpileup -d 10000 -f ref.fa sorted.bam >mpileup.txt /data/ngs/Programs/samtools-0.1.18/samtools mpileup -d 10000 -L 10000 -u -f sorted.bam > bcf.txt /data/ngs/Programs/samtools-0.1.18/bcftools/bcftools view -ANvcgbcf bcf.txt >vcf Looking forward for your reply, Thanks, Manoharan ------------------------------------------------------------------------------ Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
