Filter by alignment score [feature request]

[sjackman]

I'd like to filter out alignments with an alignment score (AS:i) less than some threshold.

[cgandini]

me 2

[cgandini]

did you found a way to do it?

[sjackman]

Yes, using awk. The following is a Makefile snippet.

# Remove alignments with an alignment score below a threshold.
%.as100.bam: %.bam
	samtools view -h -F4 $< | gawk -F'\t' ' \
			/^@/ { print; next } \
			{ as = 0 } \
			match($$0, "AS:.:([^\t]*)", x) { as = x[1] } \
			as >= 100' \
		| samtools view -@$t -b -o $@

https://github.com/sjackman/picea-sitchensis-mitochondrion/blob/master/Makefile#L288