Filtration of paired reads with both length higher than 50 from bam file

I understand that for filtering reads based on length i can simply use:

 samtools view -h file.bam | awk 'length($10) > 50 || $1 ~ /^@/' | samtools view -bS - > output.bam

But how can i select paired reads that both are longer than 50?

bam awk sed

• 1,677 views • link

updated 4.9 years ago by GenoMax

• written 4.9 years ago by Mgs3 •

Untested but may also work. Using BBMap suite.

samtools sort -n -o - file.bam | reformat.sh -Xmx6g in=stdin.bam out=filtered.bam minlength=50 requirebothbad=f

• 0 views • link

written 4.9 years ago by GenoMax

1 answer

using samjdk with option --pair:

$ java -jar picard.jar SortSam I=in.bam O=/dev/stdout SO=queryname | \
   java -jar dist/samjdk.jar --pair -e 'return records.stream().allMatch(R->R.getReadLength()>50);'

• 0 views • link

written 4.9 years ago by Pierre Lindenbaum

More posts like this

filter reads based on mapped length
written 2.1 years ago by marco.barr •

Hi everyone, I’m trying to filter reads based on their mapped length, for example from 1000 bp onwards. Could you suggest something? Would these commands …
Extract reads overlapping a specific region in bam file
written 5.2 years ago by User000

Hello, ref --------------start-----------------------------------------stop------------------------------- r1 ------------------------------------------------------- r2 --------------------------------------------------------------- r3 ----------------- -------------------------------------- r4 ----------------------------------------------------------------------------- a. I would like to extract reads from bam file that overlap entirely …
How can I filter RNA-seq reads to remove reads where more than 50% of the read is low quality (Q<20…
written 6.2 years ago by mar77 •

I'm trying to filter out any reads that consist of more than 50% low quality reads (Q<20). I've already performed filtering steps to remove adapter …
How to split paired end read as length distribution like (0-50,50-150, >150)?
written 8.2 years ago by siqizhao2018 •

hi,I want to split paired end read as length distribution like (0-50,50-150, >150),How can I do it? when I using samtools extract reads samtools view …
samtools - Finding Average Fragment size for pair?
written 8.4 years ago by oars

I'm trying to find the average fragment size for reads in my .bam file and want to also exclude read pairs with a fragment size …
Paralellize samtools piped with awk
written 8.7 years ago by Korsocius

Dear all, I have question. I would like to parallelize one line command. Could you help me please? ls 4*.bam | parallel --pipe -j 4 …
Extract reads where both pairs maps properly and none of the pairs are split from a bam file
written 9.0 years ago by rimjhim.roy.ch

Hi, I want to extract only those reads from bam file in a given region where both pairs are mapped properly and are not split. …
samtools mpileup empty when filtering out flags
written 9.2 years ago by 14134125465346445

I have a bam file of alignments to a small synthetic set of sequences, and I am heavily filtering reads that are not paired and …
featurecounts vs samtools view
written 10.8 years ago by tonja.r

I needed to check the results coming from featureCounts from subread. In fact, samtools outputted less reads then featurecounts did. I run samtools as follows: …
Filtration Of Reads With Length Lower Than 30 From Bam
written 12.5 years ago by filipzembol

<p>Dear all, I have one question how could I filtrate the reads from <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file, which have length of read lower than 30 bp. …