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16 votes
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Why does this human bam file only have one copy of each chromosome?

The maternal and paternal copies of a chromosome are called haplotypes. Many metazoans (animals) are diploid and have maternal and paternal chromosome contribution during sexual reproduction, not just ...
conchoecia's user avatar
  • 3,161
5 votes

How to differentiate DNA fastq and RNA fastq files?

welcome to the Bioinformatics StackExchange! This is one of those cases where the best solution is to just ask your collaborators. Don't bother with anything technical from the data itself because it'...
James Hawley's user avatar
  • 1,384
4 votes
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How to get unique somatic mutations for each individual patients

If what you want is to split the main VCF file into 1 file per sample, you could use bcftools query and view commands. A similar question was asked on biostars, adapting Jorge Amigo's solution to ...
cmdoret's user avatar
  • 595
4 votes
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Why are there missing calls in a VCF file from exome sequencing?

Missing variant calls due to lack of coverage shouldn't happen in the targeted capture region and I'd think most of these would come from off-target regions where some samples had reads mapped. I'd ...
Vivek's user avatar
  • 393
4 votes
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Manta "--exome: command not found"

You're missing a \ in the line before the one containing the --exome, so shell treats it as a new command, which is why you see ...
Ram RS's user avatar
  • 2,310
3 votes

How to differentiate DNA fastq and RNA fastq files?

Absolutely agree with James that you should ask your collaborators, but purely as an academic exercise... assuming you have a good reference genome+annotation (e.g. human/mouse), whole exome seq ...
Chris_Rands's user avatar
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3 votes
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How can I subset WGS data to the level of WES variants?

bcftools would be my choice, I'm sure bedtools could do the trick, too. Something along this bcftools view --regions-file or --targets, --regions-file might ...
Carambakaracho's user avatar
3 votes

Why are there missing calls in a VCF file from exome sequencing?

I've just been generating data like this, so can tell you about why/how missing calls are created in my dataset. There are two main reasons: 1. Sequencing failure When reads don't map across the ...
gringer's user avatar
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2 votes
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How do I validate a single sample ArrayCGH result?

Why not just good old qPCR? That's (A) quick, (B) cheap and (C) easy to analyze. If you care about the exact location of the break point (I'm guessing from the context that you don't), then targeted ...
Devon Ryan's user avatar
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2 votes
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Is it possible to check if a patient has the HLA-B27 antigen from his exome stored in a VCF file

Some papers claim that you can do HLA typing from exome sequencing data. I have not validated this myself. I also guess it depends on capture. Nonetheless, I don't think you can type HLA with VCF ...
user172818's user avatar
  • 6,515
2 votes
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GRCm37-designed exon target enrichment, which reference to use?

The only possible issue with using GRCm38 as the reference is that since GRCm37 was used in the bait design there are likely a few probes that will show artificial structural variations, due to errors ...
Devon Ryan's user avatar
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2 votes
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What should GC coverage bias plot of exome data look like?

Am I missing something? Should I, for instance, use my target regions instead of the reference genome? Yes you should do this. Why do you think it's wrong doing that? It should be the first thing to ...
Supertech's user avatar
  • 606
2 votes

How can I subset WGS data to the level of WES variants?

I'll expand slightly on the previous answer. First print off the positions for the exome file and then use bcftools view to filter the variants from the whole genome file. You could also index the ...
user438383's user avatar
  • 1,679
1 vote

What should GC coverage bias plot of exome data look like?

Just to formalise my comments. @Supertech's is the right answer. Background The one thing that is unusual is that the bias peaks at around 75%. The only time I've seen strong GC% bias is for ...
M__'s user avatar
  • 12.3k
1 vote

Allele frequency gnomad data

I don't do eukaryotes, well humans anyway, but in population genetics an allele frequency of zero simply means it is present in no individuals against the reference allele. It doesn't mean the allele ...
M__'s user avatar
  • 12.3k
1 vote
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What are the columns in bedtools coverage output hist file?

Found it, it is an extended .bed file format, so not specific to bedtools output: source bed file output. With 4 added columns to the end from bedtools -hist option: bedtools -hist option
Dandelion's user avatar
  • 313
1 vote

Calculating the number of probes for a given genomic range

Regardless of what your specific data is, the goal of your analysis is really to find overlaps between two data frames of genomic coordinations. My favorite package for doing this is GenomicRanges. It ...
Phoenix Mu's user avatar
1 vote

Phasing partially phased genomic data

Answer from @user438383, converted from comment: I would recommend checking out shapeit4 as it is able to integrate statistical phasing and read-based phasing like you are after. The manual page for ...
1 vote

Read-informed statistical phasing

shapeit4 is currently (probably) the most accurate and quickest phasing algorithm which can account for sequencing reads in the model. They suggest you extract the phase information from the reads ...
user438383's user avatar
  • 1,679
1 vote

What is a good pipeline for using public domain exomes as controls?

I gather that you want to use the background SNP frequency as a prior for input to your SNP calling algorithm? I'm not sure of a canned algorithm for doing this, but a quick google shows up some ...
Dan's user avatar
  • 612

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