Where can I find which read filters that are applied by default in Haplotypecaller in GATK4? (GATK web page or github page)
They hopefully will be available soon. Keep an eye on this ticket for more information.
No updates in the ticket?? Any new documents on the default read filters used in GATK4??
You can find information on read filters here: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/#ReadFilters
They seem to be all the possible read filters (42 in total) present in GATK4.I wanted the default ones that are applied automatically while processing the BAM files in Haplotypecaller. There was an old document for an older version of GATK, but none for the new one.
I have asked he dev team for an update on this. Maybe posting in this issue ticket might help the process along. Also keep an eye on it for updates. Sometimes these things fall through the cracks so thank you for bringing this to our notice.
Thanks @bhanuGandham..looking forward to it..