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Using Samtools With Many Positions

Hi,

If one position such as chr8:125976061-125976501, then the command is prety straight forward. In Linux:

samtools view -o out input.sam chr8:125976061-125976501

However I have many positions in a list file, is there a batch way to do it? The list file format likes

Chr      start      end
15       10000    20000
15       20000    30000
15       30000    40000
15       40000    50000

Thanks for help.

samtools
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updated by brentp brentp • written by Zhshqzyc • Zhshqzyc

1 answer

If it's bed format (and yours appears to be other than the header):

samtools view -L some.bed some.bam

EDIT:

though I get different results between the 2 calls:

$ cat t.bed 
chr1    1000    2000

$ samtools view -L t.bed methylcoded.bam | wc -l
1

$ samtools view methylcoded.bam chr1:1000-2000 | wc -l
22

I dont know why that is.

• 1 views • link
written by brentp brentp

Thanks, I wrote a script to reslove it.

• 0 views • link
written by Zhshqzyc • Zhshqzyc

Perhaps it's because bed files are 0 based and samtools positions are 1-based?

• 0 views • link
written by Gww Gww

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