How to simply extract certain filed from sam file

Hello everyone.

I have a sam file and only want to keep the read name and the FLAG field. How can I make it with awk?(And I do not want to keep the header)

Thanks for your answer!

sam assembly samtools

• 2,451 views • link

updated 8.3 years ago by swbarnes2

• written 8.3 years ago by 934963534 •

1 answer

How I'd do it:

samtools view mydata.bam | cut -f 1,2 > truncated.sam

• 1 views • link

written 8.3 years ago by swbarnes2

It works! Thanks a lot.

• 1 views • link

written 8.3 years ago by 934963534 •

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

• 1 views • link

written 8.3 years ago by WouterDeCoster

sorry to bother again but I wonder if there is a way to speed up this process since my sam file is 140G and it is running really slowly...

• 1 views • link

written 8.3 years ago by 934963534 •

More posts like this

Merge and unique multiple complete sam files from identical fastq files
written 1.3 years ago by JustinZhang •

**1. Background** **input**: X.R1.fq.gz, X.R2.fq.gz, GRCh38.fa I'm trying mapping X.R1.fq.gz and X.R2.fq.gz to GRCh38.fa using [last](https://gitlab.com/mcfrith/last) 3 times, with 3 seeding schemas (BISF, BISR, NEAR), …
Any option in bwa mem aligner for headless sam output?
written 3.9 years ago by robjohn70000

Hi, In the bowtie2 implementation for read alignment to a reference, there is an option (**--no-sq** Suppress @SQ SAM header lines.) to obtain a headless …
Plink: --keep flag
written 5.1 years ago by Swetaleena •

I want to subset my genotype files (ped and map) to get the data for a few samples only. I used the --keep flag from …
Find and replace the RNAME field in BAM/SAM file
written 5.2 years ago by Begonia_pavonina •

Hello everyone, I wish to change the name of the contigs in a SAM file. For this, I have to change each line of the …
How to use pacbio reads to join contigs
written 8.3 years ago by 934963534 •

Hello everyone! I have some pre-assembled contigs and want to join and extend the contigs using pacbio reads. I tried DBG2OLC on the contigs but …
Obtaining read group information from the Fastq file
written 9.4 years ago by sktbanerjee1 •

Hello everyone, I am new in the field of computational biology and I am working with few paired end fastq files with the aim of …
BWA vs Bowtie2 output
written 11.2 years ago by kimaebeloe •

Hi, I'm new in this business, but I hope my question make sense :) I'm trying to compare the output from BWA and BT2 from …
sam header is not recognized by awk?
written 11.7 years ago by mosquitoes •

Why doesn't awk recognize the sam header? I match on `^@` and it will print to stdout but not to a file. It prints to …
Bioawk: multiple criteria
written 11.7 years ago by bongbang •

From the example: awk -c sam 'and($flag,4)' aln.sam.gz How can I add `and($flag,64)` as another criterion? None of the various syntaxes I tried works. Thanks
Tool: Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
written 14.1 years ago by Istvan Albert

**Bioawk** is an extension to Brian Kernighan's awk created by [Heng Li][1] that adds support for several common biological data formats, including optionally gzip'ed BED, …