Truncating BAM Files
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6.9 years ago
JameB11 ▴ 10

Hello,

I am trying to create a smaller BAM file from the original BAM file. The smaller BAM file should have info on only about 10 loci.

Can I not just append the mpileup() output of the region of interest to the header (samtools view -H <bam>)?

Any pointers on how I can accomplish this would be appreciated!

Thanks

bam sam RNA-Seq samtools pysam • 1.8k views
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samtools view with option '-L your.bed' http://www.htslib.org/doc/samtools.html

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Sorry, but I don't have a .bed file. Just a BAM.

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Pierre meant a bam file, not a bed one. Notice he uses samtools view
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I executed the following but I get no output.

echo "Chr1:3631-5899" > test.bed
samtools view accepted_hits.bam -L test.bed
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That's not a bed file. echo -e "Chr1\t3631\t5899" > test.bed would make a valid BED file.

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