• 0 views
•
link
written
by
Pierre Lindenbaum
Extracting reads from multiple regions
Hi,
I want to extract reads from bam file using Samtools view from multiple regions.The regions I have are present in the VCF file,which I want to use.So there are not a small number of regions.Is there any way to do this in Samtools view.
for e.g inputting a file in some format in Samtools view?
Thanks
1 answer
Hello Ron!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!
PS: duplicate of "Samtools And Region List"
• 0 views
•
link
written
by
Pierre Lindenbaum
convert VCF to bed: How To Convert The Coordinates When Turning A Vcf File Into A Bed File
• 0 views
•
link
written
by
Pierre Lindenbaum
Log in to answer this question.
More posts like this
-
Extract single chromosome reads from Bam file
written by marco.barr •
-
Export sequence from specific region from bam file.
written by malkomalktho •
-
Splitting human bam file into fixed regions
written by irfanwustl •
-
Extract Reads From A Bam File That Fall OUTSIDE A Given Region
written by irfanwustl •
-
samtools view extract from .bed list to .bam file
written by matthews.alix •
-
bcftools multiple commands
written by Filago •
-
extract unmapped pair end read from sam files
written by Bioinfonext
-
extracting spesific sequences from bam or bam.bai file using samtools
written by blooming.daisy333 •
-
Merge vcf files from Multiple Samples
written by Ron
-
Extract Alignment From Very Large Bam File
written by Plantae
