User: seta

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seta1.0k
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Posts by seta

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Comment: C: Getting allele frequency and zygosity information from several vcf file
... Hi Kevin, Thanks for backing to me. I tested it on an example vcf file and it worked well on the vcf file without normalization. Best, Seta ...
written 1 day ago by seta1.0k
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Comment: C: Getting allele frequency and zygosity information from several vcf file
... Hi Kevin, Many thanks for your kind message. I'm going to use GATK for this purpose, however, as I mentioned before, this tool doesn't tell us which samples are homo and which are hetero, unlike your script. So, I'm happy if you please let me know when you modify your script. Kind regards, Seta ...
written 4 days ago by seta1.0k
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Comment: C: Getting allele frequency and zygosity information from several vcf file
... Thank you, Kevin for your explanation and link. so, the multi-allelic site has a long story. However, as I mentioned the gatk (variants to table) correctly computed hetero and homo at these positions, however, this tool doesn't say which samples are homo and which are hetero, it may be a good idea t ...
written 6 days ago by seta1.0k
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Comment: C: Getting allele frequency and zygosity information from several vcf file
... Thanks Kevin, of course, I know it. so sorry, My question is: we have not any ref allele in the real (original) vcf file (all calls are as 1|2, 2|1 and 2/2). So, how it is generated in the normalized vcf file during splitting and counted by your script, what information used for calling this homRef ...
written 6 days ago by seta1.0k
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Comment: C: Getting allele frequency and zygosity information from several vcf file
... No problem. I also try to get this information from gatk (variants to table function), and it returned me 2 AltHet and 1AltHom, like what we can see in the vcf file (original vcf file). Yes, your script is correct based on normalized vcf file. however, I'm confused with real (original) vcf file as h ...
written 6 days ago by seta1.0k
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Comment: C: Getting allele frequency and zygosity information from several vcf file
... Here, it's the original vcf file at multi-allelic site: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 As you can find, we have not RefHom in the ori ...
written 6 days ago by seta1.0k
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Comment: C: Getting allele frequency and zygosity information from several vcf file
... Actually, I run the norm command before running the script and as you can find below, the variants splited HR POS ID REF ALT AltHetCount AltHomCount RefHomCount 20 1110696 rs6040355 A G 2 0 1 20 1110696 rs6040355 A T 2 1 0 However, the count in the second row is correct. however, we co ...
written 6 days ago by seta1.0k
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Comment: C: Getting allele frequency and zygosity information from several vcf file
... No, my organism is human, and it is a multiallelic site. so, your script is fit for me, but how we can handle such sites? Thanks a lot for the link, I try it for AF and MAF. ...
written 7 days ago by seta1.0k
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Comment: C: Getting allele frequency and zygosity information from several vcf file
... Hi Kevin, Thank you so much for your helpful response. First, I normalized vcf file by bcftools norm –m-any and tried your command on the very small vcf file containing just 3 samples and found a strange thing. One of rows in my vcf file is: 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0. ...
written 7 days ago by seta1.0k
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Getting allele frequency and zygosity information from several vcf file
... Dear all, I have multiple vcf file and want to extract allele frequency and the hetero- and homozygous call with their count. Could you please let me know if I should merge all vcf file to get one vcf file, and then extract the required information? If yes, I read CombineVariants from GATK do this ...
vcf allele frequency zygocity written 8 days ago by seta1.0k • updated 8 days ago by Kevin Blighe28k

Latest awards to seta

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Popular Question 8 days ago, created a question with more than 1,000 views. For Differentially expressed gene clustering
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Popular Question 12 weeks ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list
Popular Question 3 months ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list
Popular Question 3 months ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list
Popular Question 3 months ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list
Popular Question 3 months ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list

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