Moderator: Jorge Amigo
Jorge Amigo ♦ 11k
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- Santiago de Compostela, Spain
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- https://www.researchga...
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- Joined:
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Scrutinizing genomic human variation by dealing with high throughput genotyping and next generation sequencing results, among many other things.
Bioinformatician @ Genomic Medicine Group
Hospital Clínico Universitario, Santiago de Compostela, Spain
Posts by Jorge Amigo
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... thanks for pointing it out. I've corrected my previous answer and tested thoroughly the new one. ...
written 4 months ago by
Jorge Amigo ♦ 11k
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... note that the merging process when normalizing can be quite intense on such large files as gnomad's, so if you are interested in particular regions do not forget to indicate this in your normalization command. I've edited my answer to reflect this. ...
written 5 months ago by
Jorge Amigo ♦ 11k
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... I have always used vcf.gz, although I've seen vcf.bgz probably to indicate that the compression has been performed with the `bgzip` algorithm rather than simply `gzip`. but this is simply informative for the human user, not for the software. ...
written 5 months ago by
Jorge Amigo ♦ 11k
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... [bcftools' documentation][1] is very clear about this
> Use -m2 -M2 -v snps to only view biallelic SNPs.
so if it isn't working it must be either a problem with `bcftools` (that'd be odd) or either a problem with gnomad data.
if you query gnomad data for that particular position you'll see th ...
written 5 months ago by
Jorge Amigo ♦ 11k
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... that's precisely what `-header` option does. the above command `bedtools unionbedg -i *.bedgraph -filler NA -header` does exactly what you need. ...
written 6 months ago by
Jorge Amigo ♦ 11k
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Comment:
C: bwa mem on a bam file
... from [bwa manual page][1]:
> If -p is used, the command assumes the 2i-th and the (2i+1)-th read in reads.fq constitute a read pair (such input file is said to be interleaved)
but unfortunately `samtools fastq` does not output interleaved reads.
you can either try sorting reads by name BEFORE ...
written 7 months ago by
Jorge Amigo ♦ 11k
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... my answer was very simple. this one adds more *grep* functionality: `-F` option looks for fixed strings rather than regular expressions, and `-w` option looks for whole words rather than just matching patterns. I don't know how `-F` works in conjunction with `-w`, but it looks like an overall faster ...
written 7 months ago by
Jorge Amigo ♦ 11k
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... just create a simple script.pl file containing this (do not use!)
while (<>) { chomp unless /^>/; print }
EDIT: the previous code is wrong. use this one into script.pl instead:
while (<>) { $. > 1 and /^>/ ? print "\n" : chomp; print }
and run it
perl script.pl ...
written 8 months ago by
Jorge Amigo ♦ 11k
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... update: *bcftools isec* does exactly these kind of comparisons, and faster. this quick example
bcftools isec -p isec_results file1 file2
generates in a *isec_results* folder vcf files with private variants from *file1*, private variants from *file2*, *file1* variants shared with *file2*, and * ...
written 11 months ago by
Jorge Amigo ♦ 11k
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Answer:
A: h38 total genes ?
... locate refGene file, uncompress it, look for the 13th column containing gene names, make sure there are no repetitions, and count them:
curl http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz \
| zcat | cut -f13 | sort -u | wc -l
28054 ...
written 13 months ago by
Jorge Amigo ♦ 11k
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For A: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
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For A: Which Version Of Gatk Do People Use
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For A: Which Version Of Gatk Do People Use
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For A: Filtration of bam file but with header
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13 months ago,
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For A: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
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