Hi I'm calling raw variants with the intent of using them for base re-calibration and have noticed that for some sites HaplotypeCaller gives me this warning.
I have whole genome seq data for 23 diploid individuals, 11 from one subspecies and 12 from another.
Gen size is 1.2G, and they are all male songbirds. I do have a ref genome but no gold vcf.
I would like to know what's the suggestion. That I leave the max alt alleles at 6 as the default for the program or that I change this to accommodate more alt alleles.
java -jar /users/mfariasv/data/mfariasv/install/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -T HaplotypeCaller -R newzf20/GCF_008822105.2_bTaeGut2.pat.W.v2_genomic.fa -I RSFV1A_match.bam
-I RSFV1Z_match.bam -L NC_044998.1 --genotyping_mode DISCOVERY --output_mode EMIT_ALL_SITES -stand_call_conf 30 -mbq 20 -hets 0.006 -nct 4 -o raw_variantsZF_NC_044998.1.vcf
Please sign in to leave a comment.