User: harold.smith.tarheel
harold.smith.tarheel • 4.6k
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Posts by harold.smith.tarheel
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... From the command description:
"A filtered VCF in which passing variants are annotated as PASS and failing variants are annotated with the name(s) of the filter(s) they failed."
In the SNP example you posted, it's annotated as 'PASS' - as it should be. ...
written 6 weeks ago by
harold.smith.tarheel • 4.6k
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... [VCFtools][1] '--diff' command can be used to compare VCFs for unique and shared variant calls.
[1]: https://vcftools.github.io/index.html ...
written 7 weeks ago by
harold.smith.tarheel • 4.6k
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... [VCFtools][1] '--freq' flag will output allele frequencies; you can then parse those values using 'awk' to replace the genotype call.
[1]: https://vcftools.github.io/man_latest.html ...
written 9 months ago by
harold.smith.tarheel • 4.6k
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... (note: relying on memory)
1. I believe I16 values comprises only high-quality (>Q13) bases, while the DP value is for all bases.
2. 'mpileup' calculates genotype likelihoods based on the frequency of REF vs ALT bases. To determine the actual variant (including the number of reads used to call th ...
written 10 months ago by
harold.smith.tarheel • 4.6k
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... PCR-based methods (as opposed to ligation) will produce directional libraries. You can either incorporate the Illumina adapter sequences into your amplicon primers, or add them via two rounds of PCR (first round with amplicon primers, second round with Illumina adapters + amplicon overhang). ...
written 10 months ago by
harold.smith.tarheel • 4.6k
4
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... Adding to @h.mon's answers:
2) Minor correction: the top PHRED score is 41 (ASCII character 'J' in Sanger format).
4) The instrument is programmed to sequence +1 cycle relative to the desired read length. This additional nucleotide is used for phasing/prephasing base-call correction.
5) Quality s ...
written 11 months ago by
harold.smith.tarheel • 4.6k
3
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2
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... The difference is RNA vs DNA. The histone genes are repetitive. There are four identical copies (plus several nearly identical ones) of this gene in the genome (DNA). The accession numbers you list are RefSeq RNAs for those four copies. So each (identical) RNA maps to multiple loci - and, conversely ...
written 11 months ago by
harold.smith.tarheel • 4.6k
2
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... From the [BEDtools 'intersect'][1] documentation:
> There will likely be cases where you’d like to know which “A” features
> do not overlap with any of the “B” features. Perhaps you’d like to
> know which SNPs don’t overlap with any gene annotations. The -v (an
> homage to “grep -v”) op ...
written 12 months ago by
harold.smith.tarheel • 4.6k
1
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... Ribosomal RNA contamination is common for RNA-Seq, and the genes encoding rRNA are tandem repeats.Check to see if that's the reason. ...
written 15 months ago by
harold.smith.tarheel • 4.6k
0
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2
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475
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... BEDtools will get you 90% there:
bedtools genomecov -ibam FILE.BAM -bg | awk '$4 > 249' > OUTPUT.BG
bedtools intersect -a TARGET.BED -b OUTPUT.BG -wao > OVERLAP
The first command reports the regions in your BAM with the desired coverage, the second reports the number of basepairs ...
written 16 months ago by
harold.smith.tarheel • 4.6k
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