User: nute11a

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nute11a0
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Posts by nute11a

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Comment: A: How to get GQX annotation in vcf file
... Hi Clare, I have a similar question. Were you able to find a solution? ...
written 3 months ago by nute11a0
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Answer: A: Filter heterozygous SNP calls out of a VCF file?
... Hey! I figured it out -- sorry for the late response. I used GATK and did isHet and then set filtered genotypes to no call. Thank you for your help. ...
written 3 months ago by nute11a0
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Filter heterozygous SNP calls out of a VCF file?
... Hello, I was wondering if there was a way to filter out heterozygous SNP calls from a VCF file. I am working with a model that has a doubled haploid genome, so we expect all calls to be homozygous, and any heterozygotes are a false positive which should be removed. Should I be filtering by genotype ...
vcf snp written 4 months ago by nute11a0
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Comment: C: loading plink format (generated by vcftools) file into Haploview
... Hello! I was trying to execute this command using PLINK v1.07 with this command. My file contains only SNPs. plink --file --recode HV --out which returned this: ERROR: Problem parsing the command line arguments. As far as I can tell from the manual, my usage is correct...am I missing something ...
written 6 months ago by nute11a0
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Comment: C: In vcf-contrast what do 'NOVELGT', 'NOVELAL' and 'NOVELTY' mean?
... I have the same question. Can anybody help? ...
written 6 months ago by nute11a0

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