User: QVINTVS_FABIVS_MAXIMVS

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Posts by QVINTVS_FABIVS_MAXIMVS

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Comment: C: Documentation on VCI files? Or convert VCI to VCF?
... Thanks a ton, this is what I was looking for. ...
written 21 days ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Comment: C: Documentation on VCI files? Or convert VCI to VCF?
... Diversity Outbred cohort of mouse lines that are derived from 8 founder strains. These mice are extremely genetically diverse, like a SNP every 600bp. I found this file from a FTP server for a lab at Jax ...
written 21 days ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Documentation on VCI files? Or convert VCI to VCF?
... I never came across a VCI file and I'm having some trouble finding documentation on the format. Is anyone familiar with these files? Is`ANCHOR` the reference allele, why is it absent for some variants? This is from one of the founders for the DO mouse lines. ##CREATION_TIME=05/23/2016 18:21: ...
vcf vci written 21 days ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Comment: C: Concat VCFs with some shared samples
... Because the merge tools do not like the duplicate sample names. And if you `--force-samples` then you get a second column of the sample name `NA12878` becomes `2:NA12878` and that's more of a headache . I'm looking for a quick fix out of laziness. This can be done with a quick script, but I have sp ...
written 25 days ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Comment: C: 1000Genome SV integrated map's power for SV filter
... The link to AnnotSV seems to be broken. If you are an author on the paper, do you mind fixing the link please? www.lbgi.fr/AnnotSV/ ...
written 25 days ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Concat VCFs with some shared samples
... Say I have 24 VCFs (chrom 1-Y) and I want to concat them all into one VCF. But ... for 16 VCFs I have 100 samples and for the remaining I have 95. The 95 samples are present in the 100 sample VCF. So is there an easy way to concat (not merge) these VCFs into one? ...
vcf concat bcftools written 25 days ago by QVINTVS_FABIVS_MAXIMVS2.2k
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SNP + INDEL Merging Guidelines
... Say I have SNP INDEL calls for 1000 individuals. These 1000 samples were joint-called and recalibrated with GATK in 10 batches. As a result I have 10 VCF files with SNP and INDEL calls that I would like to merge. I only have access to the VCF files, so re-calling from the BAMs is not an option. ...
vcf indel snp merging written 5 months ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Comment: C: When should you left-align INDELs (and why?)
... Thanks for the clear answer. Do you recommend `vt` or `bcftools` for normalization? ...
written 6 months ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Comment: C: When should you left-align INDELs (and why?)
... Edited the main query above. ...
written 6 months ago by QVINTVS_FABIVS_MAXIMVS2.2k
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When should you left-align INDELs (and why?)
... Say I have two VCFs with 100 samples in each file. Each VCF was joint-called separately and now I want to merge the variant calls. Do I need to left-align the INDELs in the merged VCF? I've used `bcftools norm` in the past and got odd results. It seems that `vt` is a better tool for this. Is lef ...
indel vcf left align written 6 months ago by QVINTVS_FABIVS_MAXIMVS2.2k

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