User: igorm

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igorm10
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Posts by igorm

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Comment: C: Variation of the genotypes of the human MT chromosome
... Appreciate the answer. I looked at MPSD and for all humans and it is 61 pairwise differences on average across the entire mt, which makes it ~99.6% concordance. Thanks. ...
written 6 weeks ago by igorm10
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Variation of the genotypes of the human MT chromosome
... Hi, What is the variation of the genotypes of the chrMT between random individuals? I can't find a source on this topic. I have been comparing 4 random unrelated samples and I get a concordance around ~99.5% when comparing the gt across the entire mt. Is it reasonable to expect similar concordanc ...
mitochondria chrmt variation written 6 weeks ago by igorm10 • updated 6 weeks ago by Gabriel R.2.7k
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Answer: A: Calling chrMT only from BAM
... I ended up using samtools and bcftools like so: samtools mpileup -uf human_g1k_v37.fasta sample.bam --region MT | bcftools call -m --ploidy 1 > sample_mt_only.vcf This puts the entire MT in vcf. If I would supply "-v" parameter to bcftools, it would only store the variants. samtools - ...
written 6 weeks ago by igorm10
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Calling chrMT only from BAM
... Hi, Is there a straight forward way to call variants from aligned BAM file only for the mitochondrial chromosome? Thanks ...
variant calling assembly mt written 3 months ago by igorm10

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Scholar 6 weeks ago, created an answer that has been accepted. For A: Calling chrMT only from BAM

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