Using Samtools With Many Positions

Question

[Zhshqzyc]

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.

Answer 1

[brentp]

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.

[Zhshqzyc]

Thanks, I wrote a script to reslove it.

[Gww]

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