User: hellbio

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hellbio420
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Posts by hellbio

<prev • 102 results • page 1 of 11 • next >
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How to FLAG low quality SNPs in samtools VCF
... Dear all, I have been using the below command to remove low quality SNPs from VCF generated through samtools mpileup and bcftools. > vcfutils.pl varFilter -Q 40 -d 10 input.vcf | awk '$6>=40' > output.vcf However, how can i only flag these variants as LOWQual within the VCF instead of ...
vcf samtools written 9 months ago by hellbio420 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: SNP Count from telomeres in sliding window
... It still fails with the below error: INFO: trying MySQL /usr/bin/mysql for database hg38 Non-numeric start coordinate. See line 50 in -. (remember that chromosome names should not contain spaces.) However, if i have the chromosomes sizes in the below format is there a way without using fetch ...
written 19 months ago by hellbio420
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Comment: C: SNP Count from telomeres in sliding window
... It gives a syntax error at the semicolon after $2 : > awk: { printf("%s\t0\t%d\n%s\t%d\t%d\n", $1, bounds, $1, ($2 - bounds - 1), $2; } ^ syntax error ...
written 19 months ago by hellbio420
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Comment: C: SNP Count from telomeres in sliding window
... Here the issue is that we are working on model organism for which the telomeres are not defined and available in UCSC. Therefore, we work with an assumption of 20Mb or try 10Mb later to define the telomeres. I wonder how to do this with this assumption. ...
written 19 months ago by hellbio420
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Comment: C: SNP Count from telomeres in sliding window
... Thank you. Does the count table reports the count of SNPs from both ends of the telomeres in each chromosome? Ideally, it is only required to get the count of SNPs for example upto 20Mb from either ends of the chromosomes. The middle regions i.e. SNPs in the centromeres of the chromosomes are not re ...
written 19 months ago by hellbio420
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SNP Count from telomeres in sliding window
... Hi, I have a list of SNP genomic coordinates: a.txt chr1 12345 12345 chr1 32424 32424 chr4 23234 23234 .... .... chr22 332324 332324 I would like to find the count of SNPs i.e. from the start of the chromosomes in the genome with increasing ...
genome snp written 19 months ago by hellbio420 • updated 19 months ago by Alex Reynolds30k
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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 2.0 years ago by hellbio420
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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 2.0 years ago by hellbio420 • updated 2.0 years ago by trausch1.5k
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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 2.4 years ago by hellbio420
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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 2.4 years ago by hellbio420

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Popular Question 18 months ago, created a question with more than 1,000 views. For samtools-1.1 rmdup error
Popular Question 18 months ago, created a question with more than 1,000 views. For NGS CNVtools with no controls
Popular Question 18 months ago, created a question with more than 1,000 views. For EPACTS association analysis
Appreciated 19 months ago, created a post with more than 5 votes. For Difference Between Samtools And Gatk Algorithms
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For samtools-1.1 rmdup error
Popular Question 2.0 years ago, created a question with more than 1,000 views. For NGS CNVtools with no controls
Popular Question 2.0 years ago, created a question with more than 1,000 views. For EPACTS association analysis
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For Percentage Of Exons Covered
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Epic Question 3.3 years ago, created a question with more than 10,000 views. For Difference Between Samtools And Gatk Algorithms
Popular Question 3.3 years ago, created a question with more than 1,000 views. For samtools-1.1 rmdup error
Popular Question 3.3 years ago, created a question with more than 1,000 views. For NGS CNVtools with no controls
Popular Question 3.3 years ago, created a question with more than 1,000 views. For EPACTS association analysis
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Create VCF file from .bim, .fam and .bed file
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