Tool:Uncle PSL: BLAT to SAM conversion in Python

Question

[Botond Sipos]

https://github.com/bsipos/uncle_psl

The package performs conversion of BLAT output (PSL) to SAM format. If the -N option is used then deletions larger than the specified limit are represented by the N CIGAR operation.

Conversion was tested on simulated reads against output generated by bwa mem (under the uncle_PSL/test/data directory).