Moderator: chrchang523

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chrchang5233.9k
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Posts by chrchang523

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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... Can you retry this with a more recent build? This appears to be working properly on my end, and I recall fixing this several months ago. ...
written 6 days ago by chrchang5233.9k
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... Hi, Can you post the full .log file from your run? ...
written 7 days ago by chrchang5233.9k
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Comment: C: On the usage of Golang
... Depends on how interested you are in low-level computational details like memory layout and SIMD instructions, vs. mid- and higher-level optimizations like use of Burrows-Wheeler. Golang will save you time when you stick to the latter. C and C++ are still the best places to start if you want to di ...
written 8 days ago by chrchang5233.9k
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Answer: A: On the usage of Golang
... My recent experience is that C and C++ are still king for performant one-person projects, but Golang is a better choice for new collaborative projects. Golang computational cost is roughly 1.5x that of similarly optimized C or C++ code; that's an acceptable price to pay for mutually comprehensible, ...
written 8 days ago by chrchang5233.9k
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Answer: A: Plink: Proper file format for linkage disequilibirum
... 1. DNA has two strands, where A/T and C/G are always paired. It's redundant to explicitly track both strands, so the convention is to report just the base on the 5' -> 3' strand. So 'A' really means "A on 5' -> 3' strand, T on the opposite strand", and 'G' really means "G on 5' -> 3' stra ...
written 25 days ago by chrchang5233.9k
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Answer: A: How is imputation r2 calculated in minimac3?
... Minimac3's r-squared metric is computed off your dataset (not the reference panel), and is defined as [observed dosage variance] / [expected dosage variance, given observed allele frequency and assuming Hardy-Weinberg equilibrium]. ...
written 28 days ago by chrchang5233.9k
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Comment: C: What is a faster way than using bcftool's view to extract a population from 1000
... Some situations where you should still use other tools: - There are extra FORMAT fields like GQ and DP, and you still need to retain them (plink2 can filter on them, but it won’t save the original values). - There are {P(AA), P(AB), P(BB)} genotype likelihood triplets, and you need to retain all o ...
written 5 weeks ago by chrchang5233.9k
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Comment: C: What is a faster way than using bcftool's view to extract a population from 1000
... This requires a more recent plink2 build. Alpha 1 did not support multiallelic variants. ...
written 5 weeks ago by chrchang5233.9k
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Answer: A: What is a faster way than using bcftool's view to extract a population from 1000
... Using the files from https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 : plink2 --pfile ... --keep-if SuperPop == EAS --export vcf should be a lot faster. ...
written 5 weeks ago by chrchang5233.9k • updated 4 weeks ago by zx87545.3k
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Answer: C: Paper for Plink LD clumping 'greedy algorithm'
... This isn't explicitly described in a paper, but there are some details in the plink 1.9 documentation at https://www.cog-genomics.org/plink/1.9/postproc#clump . Specifically, the core of the greedy algorithm is described in the first bullet: > - Clumps are formed around central 'index variants ...
written 5 weeks ago by chrchang5233.9k • updated 5 weeks ago by zx87545.3k

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