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Empty VCF file after runnin gHaplotypeCaller
Hi GATK team,
I'm running HaplotypeCaller using the following command:
-T HaplotypeCaller -R all.chrs.fasta -I filename.bam -o filename.vcf -stand_emit_conf 10 -stand_call_conf 20 -nct 8 -rf BadCigar
on PacBio reads aligned to a reference genome using BWA.
I don't know why I'm getting an empty VCF file. Please find attached the log file. I see that ~50% of the reads are filtered out but the second half should produce some variants, shouldn't it? Is it a coverage issue now?
Appreciate a lot you help and thanks in advance for any piece of advice!