Hi,
I am running HC with both .g.vcf and bamout as parameters. The command executes successfully, but with warning message:
Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
I have used the following command:
java -Xmx25g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta -o Sample.g.vcf -I Sample_aligned_SO_RG_MD_IR_BR.bam -ERC GVCF -variant_index_type LINEAR -variant_index_parameter 128000 --dbsnp dbsnp_149_v37.vcf --max_alternate_alleles 3 -nda -bamout Sample.g.vcf.bam -L Regions.bed
I warning messages as:
Done. There were 38 WARN messages, the first 10 are repeated below.
WARN 08:40:42,390 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values for --variant_index_type and --variant_index_parameter
WARN 08:40:48,332 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
WARN 08:40:49,769 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller
WARN 08:41:06,382 HaplotypeCallerGenotypingEngine - location 1:1633003: too many alternative alleles found (4) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: CG.
WARN 08:50:45,511 HaplotypeCallerGenotypingEngine - location 1:120612040: too many alternative alleles found (4) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: TCCGCCG.
WARN 08:53:33,251 HaplotypeCallerGenotypingEngine - location 1:175087683-175087684: too many alternative alleles found (4) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: CT.
WARN 08:53:48,228 HaplotypeCallerGenotypingEngine - location 1:183176970-183176971: too many alternative alleles found (4) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: GTTTT.
WARN 09:00:57,775 HaplotypeCallerGenotypingEngine - location 2:118854094-118854096: too many alternative alleles found (4) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: A.
WARN 09:02:40,555 HaplotypeCallerGenotypingEngine - location 2:187529823-187529826: too many alternative alleles found (4) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: A.
WARN 09:03:10,377 HaplotypeCallerGenotypingEngine - location 2:207998878-207998880: too many alternative alleles found (4) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: ATTTTTT.
My question is why am I getting this warning (WARN 08:40:48,332 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples. WARN 08:40:49,769 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller )when I have not asked for the Inbreeding coefficient to be calculated. Also, will it pose any issues later/incorrect if I use these g.vcf files for multi-sample joint genotyping and subsequent annotation downstream.
I have been through the following link which Shiela suggested, but could not get a complete understanding.
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_annotator_InbreedingCoeff.php
Please help!
Thanks
Krittika