On 14 Dec 2016, at 11:54, John Marshall <[email protected]> wrote:
>
> On 13 Dec 2016, at 23:56, Jacob Ulirsch <[email protected]> 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that the bases at positions 1330-1340 in the outdated NC_001807.4 mitochondrial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
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