PCR duplicates are not removed in the HiC workflow

[GallVp]

Description of the bug

sandblaster is used to mark PCR duplicates and they are removed with samtools view -F parameter. However, the flag setting 2316 does not remove PCR duplicates as per https://broadinstitute.github.io/picard/explain-flags.html. The setting should be switched to 3852 so that reads with following characteristics are removed,

• read unmapped
• mate unmapped
• not primary alignment
• read fails platform/vendor quality checks
• read is PCR or optical duplicate
• supplementary alignment

Command used and terminal output

No response

Relevant files

No response

System information

plant-food-research-open/assemblyqc version 2.1.1

[GallVp]

Add parameter hic_samtools_filter_flag and set its default value to 3852.

To make the flag backwards compatible, check for its absence and if absent set the value to 3852.