User: hellbio

gravatar for hellbio
hellbio320
Reputation:
320
Status:
Trusted
Location:
Last seen:
5 days, 16 hours ago
Joined:
5 years, 9 months ago
Email:
m********@gmail.com

about me

Posts by hellbio

<prev • 94 results • page 1 of 10 • next >
0
votes
4
answers
1.4k
views
4
answers
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 8 weeks ago by hellbio320
0
votes
4
answers
1.4k
views
4
answers
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 8 weeks ago by hellbio320
0
votes
4
answers
1.4k
views
4
answers
Comment: C: Genotype count in a VCF file
... could it be possible to print the sample names as well? ...
written 8 weeks ago by hellbio320
0
votes
3
answers
538
views
3
answers
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 5 months ago by hellbio320
14
votes
3
answers
538
views
12 follow
3
answers
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 5 months ago by hellbio320 • updated 17 days ago by Pierre Lindenbaum109k
1
vote
1
answer
326
views
1
answer
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 5 months ago by hellbio320 • updated 5 months ago by Pierre Lindenbaum109k
0
votes
1
answer
561
views
1
answers
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 14 months ago by hellbio320
0
votes
1
answer
561
views
1
answers
Comment: C: Picard FilterVcf Javascript Usage
... Does the above output help? ...
written 14 months ago by hellbio320
0
votes
1
answer
561
views
1
answers
Comment: C: Picard FilterVcf Javascript Usage
... Here it is: grep "#CHROM" -m 1 BC.vcf |cut -f30,31,34 BA1 BA2 BA3 ...
written 14 months ago by hellbio320
0
votes
1
answer
561
views
1
answers
Comment: C: Picard FilterVcf Javascript Usage
... I will try to explain in a different way. The genotype for the samples BA1,BA2 and BA3 should be homozygous for the alternate allele i.e. BA1=BA2=BA3=1/1 and BA4 should be heterozygous i.e 0/1 and the genotypes for the remaining samples could be either 0/0 or ./. . In the above commands `cut -f30, ...
written 14 months ago by hellbio320

Latest awards to hellbio

Appreciated 5 weeks ago, created a post with more than 5 votes. For Difference Between Samtools And Gatk Algorithms
Epic Question 5 weeks ago, created a question with more than 10,000 views. For Difference Between Samtools And Gatk Algorithms
Student 7 weeks ago, asked a question with at least 3 up-votes. For Difference Between Samtools And Gatk Algorithms
Popular Question 4 months ago, created a question with more than 1,000 views. For samtools-1.1 rmdup error
Student 5 months ago, asked a question with at least 3 up-votes. For Difference Between Samtools And Gatk Algorithms
Good Question 13 months ago, asked a question that was upvoted at least 5 times. For Difference Between Samtools And Gatk Algorithms
Epic Question 13 months ago, created a question with more than 10,000 views. For Difference Between Samtools And Gatk Algorithms
Popular Question 13 months ago, created a question with more than 1,000 views. For samtools-1.1 rmdup error
Popular Question 13 months ago, created a question with more than 1,000 views. For NGS CNVtools with no controls
Popular Question 13 months ago, created a question with more than 1,000 views. For EPACTS association analysis
Popular Question 13 months ago, created a question with more than 1,000 views. For Create VCF file from .bim, .fam and .bed file
Appreciated 15 months ago, created a post with more than 5 votes. For Difference Between Samtools And Gatk Algorithms
Great Question 17 months ago, created a question with more than 5,000 views. For Create VCF file from .bim, .fam and .bed file
Popular Question 17 months ago, created a question with more than 1,000 views. For Percentage Of Exons Covered
Student 19 months ago, asked a question with at least 3 up-votes. For Difference Between Samtools And Gatk Algorithms
Student 19 months ago, asked a question with at least 3 up-votes. For Difference Between Samtools And Gatk Algorithms
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Percentage Of Exons Covered
Great Question 2.2 years ago, created a question with more than 5,000 views. For Difference Between Samtools And Gatk Algorithms
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Illumina Read Quality
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Percentage Of Exons Covered
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Percentage Of Exons Covered
Great Question 2.6 years ago, created a question with more than 5,000 views. For Difference Between Samtools And Gatk Algorithms
Epic Question 2.7 years ago, created a question with more than 10,000 views. For Difference Between Samtools And Gatk Algorithms
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Percentage Of Exons Covered
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Percentage Of Exons Covered

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 925 users visited in the last hour