Extract line from sam file by column
I need to extract a few whole rows from a large sam file, based on column 4. I have been trying to extract it by awk, but to no avail. Anyone able to tell me where I am going wrong?
Looking to extract column 4 with either 76563 or 115625 in it and put it in the output file. The file is of course tab delineated.
samtools view practice.sam | awk -F' ' '$4/76563||115625' output.sam
• 3,814 views
•
link
updated
by
Devon Ryan
•
written
by
zshores •
•
written
by
zshores •
1 answer
awk '{OFS="\t"; if($4 == 76563 || $4 == 115625) {print}}' practice.sam > output.sam
Obiously output.sam won't have a header. I'll leave it to you to fix that.
• 0 views
•
link
written
by
Devon Ryan
OFS is the output field separator, -F is the input field separator. You can often skip an explicit print, but being able to and it being a good idea are completely unrelated things.
• 0 views
•
link
written
by
Devon Ryan
Log in to answer this question.
More posts like this
-
samtools view extract from .bed list to .bam file
written by matthews.alix •
-
Matching gene ids in R
written by aj123
-
Generating GTF files with repalced features
written by abiuma •
-
Replace FASTA header and create tab-delimited file
written by Mimmi Ahlmén •
-
Filtering SAM file based on column numbers
written by elena.syp •
-
How to ignore truncation error with PySam?
written by O.rka
-
Extract reads where both pairs maps properly and none of the pairs are split from a bam file
written by rimjhim.roy.ch
-
Error in raw count file of .sam after alignment on GRCh38
written by Mirza.Jawad •
-
genomeCoverageBed out > mapping out
written by Siva •
-
Tool: Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
written by Istvan Albert
