How can I extract the reads that map in genomic region?

[HeyIamNuria]

Hello,
I have a bam file with the alignment of Illumina reads to a genome, and a bed file with the coordinates of some genomic regions.

I found out the coverage of these regions using Bedtools, and now I want to retrieve the reads that map in these regions, but I do not know how to get the names of the reads.

Is there any available tool to extract the reads that map in a particular genomic region?

I thought Bedtools or Samtools would have it but I cannot find it.
My only other idea is to blast the reads against these regions, but I know that the results would be different.

Thank you for your help

[dpryan]

Assuming your BAM file is sorted and indexed:

samtools view -h -L Regions.bed alignments.bam > alignments_in_regions.sam

[dexterslab]

Assuming your BAM file is sorted and indexed:

samtools view -h -L Regions.bed alignments.bam > alignments_in_regions.sam

Sorry for blatantly hijacking this thread with a follow up question:

Assuming paired-end reads, would this suggested command also extract reads wherein only one of the mates falls into the region? If not, how could I archive that?

[dpryan]

Sorry for blatantly hijacking this thread with a follow up question:

Assuming paired-end reads, would this suggested command also extract reads wherein only one of the mates falls into the region? If not, how could I archive that?

Good question. Looking at the source code for samtools, it appears that it processes reads one at a time (i.e., not as pairs). So, if only one mate in a pair overlapped a region, I expect only that read would be output and not its mate. If you need both mates, it's possible that bedops implements that (I've never looked, but wouldn't be surprised).

[HeyIamNuria]

Devon,
maybe I'm wrong but did you meant to type "-L"?
Because:

"view: invalid option -- 'L'

Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]

Options: -b output BAM
-h print header for the SAM output
-H print header only (no alignments)
-S input is SAM
-u uncompressed BAM output (force -b)
-x output FLAG in HEX (samtools-C specific)
-X output FLAG in string (samtools-C specific)
-t FILE list of reference names and lengths (force -S) [null]
-T FILE reference sequence file (force -S) [null]
-o FILE output file name [stdout]
-f INT required flag, 0 for unset [0]
-F INT filtering flag, 0 for unset [0]
-q INT minimum mapping quality [0]
-l STR only output reads in library STR [null]
-r STR only output reads in read group STR [null]
-? longer help"

[dpryan]

Yes, but it seems that you have an earlier version of samtools (0.1.17 maybe?). Try upgrading, as I know the -L option is available in 0.1.18 and 0.1.19 (the most recent).

[dpryan]

BTW, here are the options for the most recent version (0.1.19):

Usage:   samtools view [options] <in.bam>|<in.sam> [region1 [...]]

Options: -b       output BAM
         -h       print header for the SAM output
         -H       print header only (no alignments)
         -S       input is SAM
         -u       uncompressed BAM output (force -b)
         -1       fast compression (force -b)
         -x       output FLAG in HEX (samtools-C specific)
         -X       output FLAG in string (samtools-C specific)
         -c       print only the count of matching records
         -B       collapse the backward CIGAR operation
         -@ INT   number of BAM compression threads [0]
         -L FILE  output alignments overlapping the input BED FILE [null]
         -t FILE  list of reference names and lengths (force -S) [null]
         -T FILE  reference sequence file (force -S) [null]
         -o FILE  output file name [stdout]
         -R FILE  list of read groups to be outputted [null]
         -f INT   required flag, 0 for unset [0]
         -F INT   filtering flag, 0 for unset [0]
         -q INT   minimum mapping quality [0]
         -l STR   only output reads in library STR [null]
         -r STR   only output reads in read group STR [null]
         -s FLOAT fraction of templates to subsample; integer part as seed [-1]
         -?       longer help

You'll also often find the -@ option useful, at least if you ever need to make BAM files.

[martin2]

If somebody trips over this old thread ...Notably, samtools extract whole read overlapping the region of interest. If you want to extract the alignment just in the region you specified, you are out of luck. This is still a largely unsolved feature. But I found gofasta can do that while returning you modified reads back in dash-padded multiFASTA ALN file (without their INSertions relative to the reference, it just omits the inserted nucleotides). See https://bioinformatics.stackexchange...es/23003#23003 for details. Not ideal but somewhat works for me.

[Jorpena]

Following up on martin2's comment, I found that bedtools intersect is a better option if you want to extract only the reads that fully fall in the regions of interest, and it gives you way more flexibility on how you want to define the intersections. For example, to get only the reads that completely fall in the BED regions

bedtools intersect -f 1 -wa -abam BAMFILE -b BEDFILE

And if you want the read fragments that fall in the BED regions you can use the default values

bedtools intersect -abam BAMFILE -b BEDFILE

Also, the output will be a BAM file which can then be piped to samtools to do other things.