Hi SAMTools team!
Recently, I discovered that “samtools view” has an option with the “-L” flag
that does this: -L FILE only include reads overlapping this BED FILE [null] .
Out of curiosity, I’m comparing the "samtools view -L" command with the
"bedtools pairtobed” command. This “bedtools pairtobed” command is the
equivalent on the BEDTools suite to the “-L” option in SAMTools.
I have 228905056 paired-end reads. After mapping, when using "samtools", I get
2934277 overlapping with the BED file I’m using. With "bedtools pairtobed” I
get 6898655. I just checked, and all the ones from samtools are in the
pairtobed results, but not the other way (i.e. no pairtobed results are in the
samtools output).
Any idea as to why this might be? Where can I read more on how SAMTools assess
overlaps in the -L option?
Best regards,
Braulio.
Inicio del mensaje reenviado:
> De: Braulio Valdebenito Maturana <bvaldebeni...@gmail.com>
> Asunto: Question about BEDTools BEDPE format versus Samtools view -L option
> Fecha: 3 de mayo de 2018 13:13:23 GMT-4
> Para: bedtools-disc...@googlegroups.com
>
> Hi BEDTools team!
>
> First of all, I have been using BEDTools for a while, and it’s a pretty
> awesome tool. Up until now, haven’t had any concern about it. My problem is
> regarding the utility “pairtobed”.
>
> Recently, I discovered that “samtools view” has an option with the “-L” flag
> that does this: -L FILE only include reads overlapping this BED FILE [null]
> . Out of curiosity, I’m comparing the "samtools view -L" command with the
> "bedtools pairtobed” command.
>
> I have 228905056 paired-end reads. When using "samtools", I get 2934277
> overlapping with the BED file I’m using. With "bedtools pairtobed” I get
> 6898655. I just checked, and all the ones from samtools are in the pairtobed
> results, but not the other way (i.e. no pairtobed results are in the samtools
> output).
>
> Any idea as to why this might be?
>
> I’ll be writing the samtools team about this issue as I have been unable to
> find more details about how they assess the overlaps.
>
> Best regards,
> Braulio.
>
>
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