Question about SAMTOOLS command
Hi everyone,
My sam files contains only three flag values:0, 4, 16. I want to filter out the flag values of 4 and 16, so I used a pipe as follows.
samtools view -Sh -F 4 in.sam | perl -F"\t" -ane 'print if /\@/; print if $F[1] == 0' | samtools view -Sb - > out.bam
After subsequent samtools sort out.bam out.sorted and samtools index out.sorted.bam steps, I run samtools tview, but see nothing there. Is my command wrong? Any of your comments will be much appreciated. THANKS!
1 answer
Why not just samtools view -SbF 20 in.sam > out.bam? Your perl command is probably mucking things up.
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Devon Ryan
Fyi, have a look at http://broadinstitute.github.io/picard/explain-flags.html to get you numeric flag representations right, especially if you need to combine different flags.
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Why don't you use
-for-Foption of samtools to filter based on flag ?Hi Geek_y, thank you for your comment.
samtools -Fis definitely the way to go, but just for sake of completeness, one error in your perl snippet is/\@/, which should be/^@/.Thank you thackl.