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Cram output #161

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mahesh-panchal opened this issue Feb 4, 2025 · 0 comments

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mahesh-panchal commented Feb 4, 2025 •

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We need cram output to run with the Sanger pipeline.

Need to trim sequences by 5 bases

trim off the first 5 bases of those libs. This is recommended by arima and they suggest to use a simple awk-script to do that:

zcat INPUT.fastq.gz | awk '{ if(NR%2==0) {print substr($1,6)} else {print}
}' | gzip > OUTPUT.fastq.gz

Convert to cram
Make crai (cram index)

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