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Pierre Lindenbaum · @yokofakun
961 followers · 1393 posts · Server genomic.social
GitHub - option --plot-depth for samtools coverage (plot coverage instead of % covered bases) by lindenb · Pull Request #1910 · samtools/samtools

The PR for samtools (visualize CNVs in the ) was merged today ! github.com/samtools/samtools/p

#terminal #samtools #cnv #SV #structuralvariant #ascii

Last updated 1 year ago
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Pierre Lindenbaum · @yokofakun
955 followers · 1363 posts · Server genomic.social

I just wrote a new PR for `samtools coverage` to plot the depth instead of the '% of covered bases' . Useful to validate in the terminal.

github.com/samtools/samtools/p

#cnv #samtools #bioinformatics #SV #variant #bam

Last updated 1 year ago
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Pierre Lindenbaum · @yokofakun
942 followers · 1275 posts · Server genomic.social

#samtools #bioinformatics

Last updated 1 year ago
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Charles Plessy · @charles_plessy
2 followers · 22 posts · Server fediscience.org

Split a file produced by into one file per barcode, using and :

samtools view in.bam | awk '/CB:Z:/{f=substr($0,match($0,/CB:Z:[ACGT]{16}/)+5,16)".txt"}{print>>f}'

#awk #samtools #SingleCell #cellranger #Bam

Last updated 1 year ago
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Pierre Lindenbaum · @yokofakun
854 followers · 847 posts · Server genomic.social

asked "htslib/c what is the correct way to use bgzf_thread_pool ?" biostars.org/p/9551841/

#biostars #c #samtools #htskib #fastq

Last updated 2 years ago
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Pierre Lindenbaum · @yokofakun
621 followers · 449 posts · Server genomic.social

plot depth of in the using and gnuplot:

```
$ samtools depth -a -r "chr1:234-456" in.bam | cut -f 2,3 | gnuplot -e 'set terminal dumb size 120,28; plot "-" smooth csplines with lines notitle'
```

#coverage #terminal #samtools #depth #linux #bioinformatics

Last updated 2 years ago
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