BC tags with "none" value

[valeriuo]

Hi!

We found a BAM file, produced by Isaac 03.16.02.19, that contains BC tags with "none" value, which is invalid according to the standard, section 1.3. The barcodes appear to have been read from a CSV file.

This issue might be present in some of your other aligners.

[rpetrovski]

Looks like you are right. Would it help if you add BC to --bam-exclude-tags? I suppose you seen none only in the runs that don't have actual barcodes. Correct?

Roman.

[valeriuo]

I didn't run the aligner myself, so I wouldn't know if it helps. We just bumped into this strange BAM file when we added barcode statistics to samtools and we saw errors popping out of this file. I assumed it was the aligner, because the only PG line in file header showed the aligner command:

isaac-align 
--output-directory Output 
--temp-directory Temp 
--bam-gzip-level 6 
--scatter-repeats 1 
--reference-genome human-sorted-reference.xml 
--cleanup-intermediary 1 
--memory-limit 154 
--clip-semialigned 1 
--base-quality-cutoff 15 
--stats-image-format none 
--gap-scoring bwa 
--variable-read-length yes 
--ignore-missing-bcls 1 
--ignore-missing-filters 1 
--split-gap-length 10000 
--seed-length 16 
--clip-overlapping 1 
--lane-number-max 2 
--base-calls Fastq 
--base-calls-format fastq-gz 
-s sheet.csv 
--use-bases-mask Y150N1,Y150N1 
--tiles s_1,s_2

All the reads have BC:Z:none and no quality tag attached.

[valeriuo]

Also, I've looked through the Isaac code and I've see that it is possible to set the barcode to "none", if you call setSequence with an empty string.