Undersstanding these SNAP command at SURPI

Question

[always_learning]

I was just exploring SURPI at this link https://github.com/snashraf/surpi/blob/master/SURPI.sh

I was just wondering that what this line is doing exactly . [Line No 812]

snap-dev single "$SNAP_subtraction_db" "$file_to_subtract" -o -sam "$subtracted_output_file.$SUBTRACTION_COUNTER.sam" -t $cores -x -f -h 250 -d ${d_human} -n 25 -F u

I know its alignment by SNAP but what these -x, -f, -h flags are. I tried to look into snap documents here http://snap.cs.berkeley.edu/downloads/snap-1.0beta-manual.pdf as well but didn't get any related info as well.

Answer 1

[hamzakhanvit]

You can install SNAP and run snap single to display all its options. For example -
-n number of seeds to use per read -x explore some hits of overly popular seeds (useful for filtering)
-f stop on first match within edit distance limit (filtering mode)
-h maximum hits to consider per seed (default: 300)
-F filter output (a=aligned only, s=single hit only (MAPQ >= 10), u=unaligned only, l=long enough to align (see -mrl))