John -- Thank you for your quick response.
The commands -t and --skip-indels were used because I was originally
outputting to vcd, but I subsequently verified that the problem was at the
level of mpileup output. Yes, working with human -- hg19. I will check on
the two things that you mention, but the mtDNA.fasta file used to align, in
the faidx command, and in the mpileup command is in fact the exact same one
in the same location. I will get back with more details and thanks again.
Jacob
On Wed, Dec 14, 2016 at 1:16 PM, John Marshall <j...@sanger.ac.uk> wrote:
> On 14 Dec 2016, at 11:54, John Marshall <j...@sanger.ac.uk> wrote:
> >
> > On 13 Dec 2016, at 23:56, Jacob Ulirsch <julir...@broadinstitute.org>
> wrote:
> >> Here is output from faidx, showing the correct fasta sequence for these
> positions:
> >>
> >> samtools faidx mtDNA.fasta chrM:1330-1340
> >>> chrM:1330-1340
> >> GTCAAGGTGTA
> >
> > You don't say what species you're working with, but assuming human...
> In fact the bases at positions 1330-1340 in the human mitochondrial DNA
> sequence (NC_012920) are indeed CAAGGTGTAGC.
>
> After a conversation with James Bonfield and looking at this further, I
> recall that the bases at positions 1330-1340 in the outdated NC_001807.4
> mitochondrial DNA sequence are GTCAAGGTGTA.
>
> So it would appear that you have a GRCh37/hg19 mtDNA.fasta file that you
> used to align input.bam and in the faidx command shown, and a separate
> GRCh38/hg38 mtDNA.fasta file that you used in the mpileup command.
>
> John
>
> --
> 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.
>
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