different number of reads reported and in bam file about longshot HOT 5 OPEN

Hello,

Looking more closely to this issue, it appears that the bam file produced by longshot also contains supplementary and secondary alignments, even though these are filtered out before SNV discovery. Filtering these out, I get 29240 unphased reads, but I should be getting 26476, so there are ~ 3 thousand additional reads. Wat else could I be missing?

Cheers,

Juan D. Montenegro

from longshot.

Longshot does output all alignments therefore the total number of reads in the output should be exactly the same as in the input bam. The statistics are only for the filtered reads. Can you confirm if the extra reads are duplicates?

from longshot.

Hello,
Sorry for the late reply. The input and output do have the same number of records. So I am probably missing some filter to make the numbers match. Besides A30 and secondary/supplementary alignments, what else is being ignored by Longshot? I amasking this, beacuse I am usually, reassemblying the phased and unphased reads. Usually what I see is that one end of the original contig cannot be phased, while the other end is split into two homologous haplotypes, but in some cases I do get a very complex partition after assemblying, so I guess some of the unphased reads actually help complete gaps between haplotypes but were too short and did not contain enough polymorphisms to be phased.

Any help selecting the appropriate set of unphased reads would be very helpful.

Cheers,

Juan D.

from longshot.

Longshot filters out reads with low mapping quality in addition to secondary/supp. alignments. I have copied the list of filters from the code below:

record.is_quality_check_failed()
|| record.is_duplicate()
|| record.is_secondary()
|| record.is_unmapped()
|| record.mapq() < min_mapq
|| record.is_supplementary()

All these reads will be output as 'unphased'.

from longshot.

from longshot.