User: maegsul

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maegsul110
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Posts by maegsul

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
... Hi, I think I have come across with the same problem but with the below code is working well for me, maybe give it a try: return new VariantContextBuilder(variant). genotypes( variant. getGenotypes(). stream(). map( G->{ if(G.hasAD() && G.i ...
written 4 months ago by maegsul110
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Comment: C: Extracting Cumulative (Rare) Allele Frequencies for a Subset of Variants From a
... Thanks a lot Pierre! Your code helped me, but what I was looking for was something that is a bit different. I want to query the (rare) variants falling into a group (usually a gene name) from a .tsv file, not from SnpEff annotation directly. For these variants, I want to obtain cumulative MAF (so w ...
written 4 months ago by maegsul110
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Extracting Cumulative (Rare) Allele Frequencies for a Subset of Variants From a VCF
... Hi, I am conducting rare variant tests for predefined genomic units (such as genes) genome-wide, each containing a subset of variants from a multi-sample VCF. I used SKAT-O for that purpose in R, that functions reasonably well to output the rare variant test association p-values per genomic unit. ...
vcf filter rare variant tests enrichment written 5 months ago by maegsul110 • updated 5 months ago by Pierre Lindenbaum115k
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Comment: C: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
... Yes, now I understood my mistake... Now it works very well! Thank you very much once more Pierre! ...
written 6 months ago by maegsul110
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Comment: C: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
... The logic is fine with the first two options you indicated, but I couldn't manage to make it work. Still all the genotypes (regardless of being a heterozygous or homozygous ref call) are filtered based on the custom AD filter. My goal is to assign NO_CALL genotypes only for heterozygous genotypes ha ...
written 6 months ago by maegsul110
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Comment: C: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
... Yes, I marked it as accepted, thank you very much again! I couldn't figure out where to add .isHet() in the working script though, I am having some errors with the script... ...
written 6 months ago by maegsul110
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Comment: C: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
... This worked very well, thank you very much! Only thing is that, I have to modify this script only for heterozygous calls, otherwise my homozygous ref calls are also turned into NO_CALL genotype. Can I add something like .isHet(); for that purpose? ...
written 6 months ago by maegsul110
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Comment: C: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
... Thank you very much Pierre! I didn't know about vcffilterjdk - it looks very useful. However, this command above is not exactly what I wanted. It actually filtered out all of the variants (i.e. at least in one of my samples allelic imbalance is present). What I want is to assign ./. missing genotyp ...
written 6 months ago by maegsul110
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Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
... Hi, I am trying to filter my GATK 4.0.3 - HaplotypeCaller generated multi-sample VCF for allele depth (AD) annotation at sample genotype-level (so available in "FORMAT" fields of each sample). I think prior to GATK 4, this annotation was available as "Allele Balance" (AB) ratios (generated by Alle ...
gatk allele depth filtering sequencing written 6 months ago by maegsul110 • updated 6 months ago by Pierre Lindenbaum115k
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Comment: C: IBD calculation indicates cryptic relatedness of 1 Individual with all others wi
... Thank you for your reply! Actually I already checked it with plink2 --make-king-table too and I've got these: Kinship score between siblings (confirmed) : 0.29 Kinship score between possible new pair: 0.19 Kinship score between Sample1 (with respect to my original post) and all others: varies bet ...
written 7 months ago by maegsul110

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