User: hermathena

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hermathena40
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New User
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United Kingdom
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1 week, 6 days ago
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3 years, 3 months ago
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Posts by hermathena

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Variant caller comparison for non-human data (highly varied populations)
... Thanks for this. I have experimented wth GATK v4 Beta. There are some gains in speed through multithreading. Unfortunately, there are also many bugs that crop up. Broad is recommending not using GATK4 with Spark for now. That horrible Queue parallelisation is gone, but now you need to use something ...
written 21 days ago by hermathena40
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Variant caller comparison for non-human data (highly varied populations)
... Hi, Is anyone aware of a recent comparison of various variant callers (GATK, FreeBayes, etc) for non-model organisms, please? There are many out there for human data, obviously because there are good reference sets. My data is hundreds of whole genomes from an insect species (>10% sites variable ...
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Answer: A: Getting data into Plink! and TreeMix
... Hi, Plink v. 1.9 does a very good job. You can ask it to read in vcf and --make-bed: /bin/plink2/plink --vcf input.vcf --make-bed --geno 0.25 --maf 0.01 --snps-only --out input.qual --allow-extra-chr --within my_clusters.clust Unfortunately the resulting .bim file has periods instead of SNP names, ...
written 9 months ago by hermathena40
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Comment: C: Recalculate QUAL and INFO fields for a subset of samples in a VCF
... Indeed, the FORMAT fields available are AB, AD, DP, GQ, GT, MQ0, PL. Which version of bcftools, please? ...
written 22 months ago by hermathena40
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Recalculate QUAL and INFO fields for a subset of samples in a VCF
... Dear All, I extracted some samples from a larger VCF (one population of a species). I would like to filter the sites by quality and depth. However, the values in the new VCF still seem to reflect the data from the bigger VCF (i.e. the average depth was calculated for all samples, not just the extra ...
next-gen snp written 22 months ago by hermathena40 • updated 22 months ago by geek_y8.1k
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Getting data into Plink! and TreeMix
... Dear All, I am trying to get non-model data into the software TreeMix (https://code.google.com/p/treemix/). I have data from multiple species, 1-10 individuals for each. I start with a VCF of biallelic SNPs from GATK and generate Plink input with vcftools: vcftools --vcf exon.biallelicSNPs.vcf --p ...
genome next-gen snp written 3.2 years ago by hermathena40
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Comment: A: Taking the difference of two VCFs (or removing singletons)
... Hello, Thank you all for the suggestions, this looks promising! Best, Chris ...
written 3.2 years ago by hermathena40
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Taking the difference of two VCFs (or removing singletons)
... Dear All, Is there a way to take a difference of two VCF files? GATK can be used to take a Union or an Intersection, but I need the difference. There are two applications: 1. remove singletons. I have a VCF of all the SNPs and a VCF of the private ones. I need a VCF with the non-private SNPs. 2. ...
genome filter singleton snp sequencing written 3.2 years ago by hermathena40

Latest awards to hermathena

Popular Question 21 months ago, created a question with more than 1,000 views. For Taking the difference of two VCFs (or removing singletons)
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Getting data into Plink! and TreeMix

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