Extract read names from BAM files

Question

[Mathias_H]

Hello everyone, I need to extract the names of the reads in a BAM-file. The result should be a text-file with all the read names. I did not find any command in samtools or picard which would do this task. I am working with R, so it would be best to have something which is implementable in an R pipeline.

Can anyone help me?

Answer 1

[GenoMax]

Not a solution in R but this should do it:

samtools view your.bam | cut -f1 | sort | uniq > read_names

[Mathias_H]

Thank you! Looks like it worked.

Answer 2

[Asaf]

samtools view file.bam |cut -f 1 ?

Answer 3

[swbarnes2]

I got this off of stack exchange; it's faster, because it doesn't sort

samtools view mine.bam | cut -f 1 | awk '!x[$0]++' > read.names.txt

[zx8754]

Please add the link to Stack Exchange post.

Answer 4

[Bastien Hervé]

If your bam file is very light, in R you can do :

library(Rsamtools)
bam <- scanBam("input.bam")
bam[[1]]$qname

Otherwise, command line answers are preferred