User: john.michel.rouhana

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Posts by john.michel.rouhana

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Answer: A: VCF deletions incorrectly formatted
... I wound up just parsing the vcf in Python and calling samtools to correct the deletions in the vcf. By subtracting 1 from the alleged bp_pos, calling `samtools faidx chr:del_start-del_end` for each REF, and taking the first character of that for ALT, you can fill in the blanks. I don't believe ther ...
written 20 days ago by john.michel.rouhana10
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Comment: C: VCF deletions incorrectly formatted
... I definitely agree that it's odd. I'm having trouble finding older versions that used a `-` as ALT in deletions, so I'm not sure it's ever the case. A big part of this problem is that I can't figure out how the people who supplied the VCF ended up in this situation. bcftools doesn't seem to fix the ...
written 20 days ago by john.michel.rouhana10
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VCF deletions incorrectly formatted
... Hi all, I'm working with a vcf (v4.1) that has incorrectly formatted deletions for some reason. The insertions are fine, but the deletions are annotated as (example): #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 2 32474671 indel.60227 A - . PASS . GT Notice tha ...
vcf reference panel qc written 20 days ago by john.michel.rouhana10
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Comment: C: IMPUTE2- Map file for custom reference panel
... I tried to find updated versions. What you say makes sense, and is actually the conclusion I came to (I missed the response). Once I revisit this problem I'll likely be resorting to recalculating the recombination rates if I cannot find updated files. ...
written 20 days ago by john.michel.rouhana10
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IMPUTE2- Map file for custom reference panel
... Hi all, I'm trying to build a custom reference panel for use with IMPUTE2. I have a phased .vcf from all my participants, and I was using [the first script here][1], modified slightly to work with my vcf/HG38, to build the reference panel. The exact command I run to generate the files for chromosom ...
impute2 reference panel imputation written 6 weeks ago by john.michel.rouhana10 • updated 6 weeks ago by h.mon26k
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Comment: C: Remove variants that do not map to human genome
... I wasn't aware- thank you for making this apparent. I thought it'd make the most sense to post it in both locations. Thanks for the etiquette lesson. Is there any way to remove my post here? ...
written 9 weeks ago by john.michel.rouhana10
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Remove variants that do not map to human genome
... I received an hg38 VCF file that's had variants imputed with 1000 genomes. I've encountered some issues with the VCF; REF alleles that do not align to a reference genome, ALT alleles that do not appear to be reported anywhere in the literature, and, most recently, variants that flat-out do not ali ...
vcf variant-calling qc written 9 weeks ago by john.michel.rouhana10 • updated 9 weeks ago by Pierre Lindenbaum121k

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Scholar 20 days ago, created an answer that has been accepted. For A: VCF deletions incorrectly formatted

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