User: hellbio

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hellbio330
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Posts by hellbio

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Comment: C: Mendelian Inheritance Rate (CNV)
... did you find a way to do this? i am in a similar situation. ...
written 8 weeks ago by hellbio330
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Human CNV VCF for Trios from whole-genomes
... Dear all, I am looking for CNVs in father-mother-child trios generated from whole-genome sequencing data. I have searched DGV and could find data from several projects including 1000genomes project. However, the data is in gvf format which does not have a sample specific genotypes in the file to i ...
wgs cnv trios written 9 weeks ago by hellbio330 • updated 9 weeks ago by trausch1.1k
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Comment: C: Genotype count in a VCF file
... I tried getSampleName() in the print statement. It won't do what i need, it is just printing one name for all the variants. Seems there is a little more complicated solution that needs some intuition. Could you help. out.println(ctx.getContig()+" "+ctx.getStart()+" "+JSON.stringify(m)+" ...
written 6 months ago by hellbio330
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Comment: C: Genotype count in a VCF file
... Hi Pierre, could we print the sample names also in separate columns corresponding to the counts? BTW, i could not find the jar in the git, is it moved to a different location or name? ...
written 6 months ago by hellbio330
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Comment: C: Genotype count in a VCF file
... could it be possible to print the sample names as well? ...
written 6 months ago by hellbio330
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Comment: C: How to get sample names and genotype for SNP in multi-sample VCF file
... do you mean that it should be done in steps? to get counts and sample names? ...
written 9 months ago by hellbio330
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How to get sample names and genotype for SNP in multi-sample VCF file
... Dear all, I have a multi-sample (>100) VCF file and a list of SNPs with CHR and POS for which the sample names and their genotypes need to be extracted. For example, i have a SNP chr1:23455. I would like to know how many and which samples have homozygous alternate allele, heterozygous allele ...
gatk genotype snp written 9 months ago by hellbio330 • updated 4 months ago by Pierre Lindenbaum114k
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How to filter VCF where at least x% of the individuals have DP>=10 and GQ>=20
... Hi, I would like filter the vcf file using DP and GQ thresholds at sites where atleast 80% of the individuals meeting the thresholds. More precisely, i have the below two scenarios: 1. Retain sites where atleast 80% of the individuals had at least depth DP >= 10 and GQ>=20 irrespective of ...
vcf filter gatk written 9 months ago by hellbio330 • updated 9 months ago by Pierre Lindenbaum114k
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Comment: C: Picard FilterVcf Javascript Usage
... It works on a different test case where i have simulated the input to match the criteria specified in javascript. In the above case there seems to be no variant meeting the criteria in the javascript and so there is no variant in the output with flag "PASS". ...
written 18 months ago by hellbio330
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Comment: C: Picard FilterVcf Javascript Usage
... Does the above output help? ...
written 18 months ago by hellbio330

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Appreciated 5 months ago, created a post with more than 5 votes. For Difference Between Samtools And Gatk Algorithms
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Student 5 months ago, asked a question with at least 3 up-votes. For Difference Between Samtools And Gatk Algorithms
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Popular Question 17 months ago, created a question with more than 1,000 views. For samtools-1.1 rmdup error
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Popular Question 17 months ago, created a question with more than 1,000 views. For Create VCF file from .bim, .fam and .bed file
Appreciated 19 months ago, created a post with more than 5 votes. For Difference Between Samtools And Gatk Algorithms
Great Question 21 months ago, created a question with more than 5,000 views. For Create VCF file from .bim, .fam and .bed file
Popular Question 21 months ago, created a question with more than 1,000 views. For Percentage Of Exons Covered
Student 23 months ago, asked a question with at least 3 up-votes. For Difference Between Samtools And Gatk Algorithms
Student 23 months ago, asked a question with at least 3 up-votes. For Difference Between Samtools And Gatk Algorithms
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