Region "Awk" Specifies An Unknown Reference Name

Question

[Zhshqzyc]

Hello, can you look at what is wrong by using samtools command?

#!bin/bash
samtools view  -o raw_genome.txt my.bam awk '{print $3, $4, $10;}' \
raw_genome.txt >raw_sequence.txt

What I got is

[main_samview] region "awk" specifies an unknown reference name. Continue anyway.

[mainsamview] region "{print $3, $4, $10;}" specifies an unknown reference name. Continue anyway. [mainsamview] region "raw_genome.txt" specifies an unknown reference name. Continue anyway.

Thanks

Answer 1

[Pasta]

Add a pipe "|" and remove the -o option and do something like that:

samtools view my.bam | awk '{print $3, $4, $10;}' > Raw_File.txt

The pipe will redirect the output of your first command to the next command