User: Rlong

gravatar for Rlong
Rlong340
Reputation:
340
Status:
New User
Location:
US
Website:
http://partek.com
Last seen:
4 years, 8 months ago
Joined:
7 years, 6 months ago
Email:
s***************@gmail.com

Currently: Software Engineer at Partek,

twitter: @plantimals

Formerly: Programmer/Analyst at The Genome Institute of Washington University School of Medicine in St.Louis, Missouri.

Posts by Rlong

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Looking For A Vcf/Bcf C++ Library
... Unfortunately, I can only be assured of having VCF/BCF files, and not necessarily the original aligned BAMs. I am working on a variant annotator, and I would like for it to able to take either VCF or BCF as input, and produce the same for output. ...
written 5.2 years ago by Rlong340
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Looking For A Vcf/Bcf C++ Library
... I am looking for a liberally licensed C++ library that can parse both VCF and BCF. I like vcflib, but it does not handle BCF. Suggestions? ...
vcf written 5.2 years ago by Rlong340 • updated 5.2 years ago by pd3310
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Comment: C: How To Switch From Samtools Pileup To Mpileup
... The "b" in the -bvcg causes bcftools to output bcf instead of vcf. You can omit the "b" or use bcftools view your_file_name_here to see the contents in plain text. ...
written 5.7 years ago by Rlong340
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Answer: A: How To Switch From Samtools Pileup To Mpileup
... From the mpileup page: samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf The -c in the bcftools view command calls SNPs. ...
written 5.7 years ago by Rlong340
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Comment: C: Finding Somatic Mutations From Whole Exome
... Do you have a matched normal sample? Without a comparison, you won't be able to tell somatic from germline mutations. ...
written 5.9 years ago by Rlong340
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Comment: C: What Are The Big Questions That Bioinformatics And Computational Biology Will Be
... This is spot on. ...
written 5.9 years ago by Rlong340
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Comment: C: Understanding Vcf File Format
... There is only one GQ value. It is 87.16 (87 and 16/100) ...
written 6.0 years ago by Rlong340
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Answer: A: Understanding Vcf File Format
... For another reference, try the 1000 genomes site. The AD stands for allele depth, GQ is genotype quality, and that is one float value. PL is the phred-scaled genotype likelihood. ...
written 6.0 years ago by Rlong340
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Answer: A: Vcftools: Vcf-Isec Error The Column Names Do Not Match.
... It looks like this tool is requiring that you use vcfs from the same sample. Since the column name of the per-sample data in VCF is the name of the sample, it is telling you that these don't match and refusing to proceed. If you include the -f option to force it, it should proceed as requested. ...
written 6.0 years ago by Rlong340
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Comment: C: Vcftools,Vcf-Merge Error
... Are you sure that "raw_s_5_1_sequence_BWT.vcf.gz" is a proper vcf and not a BAM or something else? It looks like the forward reads from lane 5 off of a flow cell.. ...
written 6.0 years ago by Rlong340

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