Simple question
Seems like the command:
samtools view -b -h <input.bam> -L <input.bed>
for subsetting the bam file to keep only those reads intersecting the seqnames and their regions in input.bed is retaining the original header in the output bam file, including those seqnames not present in input.bed.
Is there a samtools flag that can be used to tell samtools to also subset the header to keep only those seqnames in input.bed?
1 answer
Is there a samtools flag that can be used to tell samtools to also subset the header to keep only those seqnames in input.bed?
No. You would need to pipe to samtools reheader to do that.
The BAM file format differs from SAM in that RNAME is stored not as a string but as the zero-based integer offset of the match @SQ header instead of the seqname string. This means that a) BAM files must have @SQ headers, and b) any subsetting of @SQ requires rewriting all BAM records with the new offsets. samtools view does not have this capability.
Log in to answer this question.
-
Differing number of reads for read 1 and 2 in fastq's from a subset bam file
written by michael •
-
samtools view extract from .bed list to .bam file
written by matthews.alix •
-
Samtools reheader Numerical result out of range
written by Medhat
-
Samtools gives "truncated file" when trying to view a "reheaded" file
written by olavur
-
Extract reads where both pairs maps properly and none of the pairs are split from a bam file
written by rimjhim.roy.ch
-
samtools mpileup empty when filtering out flags
written by 14134125465346445
-
Trying to create short test bam not working.
written by ariel.balter
-
Truncating BAM Files
written by JameB11 •
-
Mapping shorts reads using Bowtie
written by bioinfo
-
Samtools or Bedtools: How to filter a bam file with a bed file using strand information
written by retrogenomics •
