I was trying out the filter method on my pbsv pipeline (my input reads are PacBio CCS), but I got the following error from the pbsv call on chromosome 1:
SVSIG ref size 182983494 vs fasta ref size 248956422
svsig file was generated by converting leaf output SAM to BAM and indexing after sorting. I am using the identical reference fasta for linear and pbsv.
After investigating, I noticed the SAM output from linear has different chromosome lengths.
Hi,
I was trying out the filter method on my pbsv pipeline (my input reads are PacBio CCS), but I got the following error from the pbsv call on chromosome 1:
SVSIG ref size 182983494 vs fasta ref size 248956422svsig file was generated by converting leaf output SAM to BAM and indexing after sorting. I am using the identical reference fasta for linear and pbsv.
After investigating, I noticed the SAM output from linear has different chromosome lengths.
Do you have any insights on this?