samtools return seek position
I was wondering if there is a way to return byte ranges instead of a slice with samtools view on a bam file?
In other words, with samtools view -bh foo.bam 1:10-100,
it returns a pair of ints (start_byte_pos, end_byte_pos) for the resulting query, or a list of such pairs if the data are not located contiguously in the foo.bam.
• 1,431 views
•
link
updated
by
Devon Ryan
•
written
by
peiqi1122 •
•
written
by
peiqi1122 •
1 answer
You can't get that with the command line program. If you really need that information, then I presume you're programming anyway, so you'll want to look at htslib, which underlies samtools and provides the functionality that you're looking for.
• 0 views
•
link
written
by
Devon Ryan
Log in to answer this question.
More posts like this
-
RNA-Seq - Strand-specific coverage for a paired library
written by npb27 •
-
Filter BAM by chromosome using PySam
written by pablosolar.r •
-
Samtools view does not output all reads
written by b10hazard •
-
samtools view region and include duplicate reads
written by mgene •
-
solved :use pandas dataframe column result to slice data in other columns
written by toth.joe •
-
first and second mate reports by samtools 0x40 and 0x60 FLAGs
written by R •
-
Discrepancies in Bam Read Lengths
written by jdimatteo •
-
Using samtools to print only base pairs
written by oritz1717 •
-
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
written by Istvan Albert
-
Paired-End Sequence Preprocessing Effects On Downstream Processes
written by Travis
