samsift can't find the AS tag to filter a bam file generated using bowtie2

Question

[michael.flower.14]

Using samsift I've successfully filtered bam files generated by alignment using bwa mem. However, it doesn't seem to work for bowtie2.

Here's the script:

REF="/Users/michaelflower/refs/rep/HTTset20_CAG0500.fasta"
OUT="/Users/michaelflower/my_bin/amplicon_repeat_seq/cassio_results"
FN="Flower_n7m_3_FSC1_Linear_2950"
METHOD="bowtie2"
my_sam="${OUT}/${FN}.${METHOD}.sam"
my_bam="${OUT}/${FN}.${METHOD}.bam"

bowtie2 -x "$REF" -U "$R1" -S "${OUT}/${FN}.${METHOD}.sam"

samtools sort "${my_sam}" > "${my_sam%.*}.bam"
samtools index "${my_sam%.*}.bam"
samtools flagstat "${my_sam%.*}.bam" > "${my_sam%.*}.flagstat.txt"

samsift -i "${my_bam}" -o "${my_bam%.*}.filtered.bam" -f 'AS>94'

Here's the error:

$ samsift -i "${my_bam}" -o "${my_bam%.*}.filtered.bam" -f 'AS>94'
[samsift] 2024-02-28 22:08:41 SAMsift is starting.
Traceback (most recent call last):
  File "/Users/michaelflower/micromamba/envs/bioinfo/bin/samsift", line 10, in <module>
    sys.exit(main())
  File "/Users/michaelflower/micromamba/envs/bioinfo/lib/python3.10/site-packages/samsift/samsift.py", line 418, in main
    sam_sift.run()
  File "/Users/michaelflower/micromamba/envs/bioinfo/lib/python3.10/site-packages/samsift/samsift.py", line 283, in run
    self.process_alignment(alignment)
  File "/Users/michaelflower/micromamba/envs/bioinfo/lib/python3.10/site-packages/samsift/samsift.py", line 248, in process_alignment
    self._filter()
  File "/Users/michaelflower/micromamba/envs/bioinfo/lib/python3.10/site-packages/samsift/samsift.py", line 182, in _filter
    self.passes=eval(self.filter, self.vardict)
  File "<string>", line 1, in <module>
NameError: name 'AS' is not defined

I had a similar issue with minimap2 that was solved by adding the --sam-hit-only tag.

I can't find an answer online or on readmes, so any help would be great!

[Pierre Lindenbaum]

what is AS ? an attribute in a SAM record? Are you sure this is the way to access an attribute : -f 'AS>94' . Otherwise, just use samtools view --expr 'something'