Hi,
I am new to GATK and bioinformatics, so I have some basic questions to ask about some warnings I ran into. I am following RNAseq short variant discovery (SNPs + Indels) on GATK website [https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels-]. When I run the following command:
gatk HaplotypeCaller \
-R $HG19_DIR/hg19.fa \
-I $FILE_OUT.step6.bam \
-O $FILE_OUT.g.vcf.gz \
-ERC GVCF
I got tons of following warnings and only few genotype positions are processed:
12:03:50.537 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
12:03:50.537 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
12:03:50.538 INFO IntelPairHmm - Available threads: 1
12:03:50.572 INFO IntelPairHmm - Requested threads: 4
12:03:50.576 WARN IntelPairHmm - Using 1 available threads, but 4 were requested
12:03:50.577 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
12:03:50.692 INFO ProgressMeter - Starting traversal
12:03:50.699 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
12:03:53.673 WARN DepthPerSampleHC - Annotation will not be calculated at position chr1:367878 and possibly subsequent; genotype for sample Jagadeesh_64bit/MGH3006v2 is not called
12:03:53.673 WARN StrandBiasBySample - Annotation will not be calculated at position chr1:367878 and possibly subsequent; genotype for sample Jagadeesh_64bit/MGH3006v2 is not called
12:03:53.680 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1:367878 and possibly subsequent; at least 10 samples must have called genotypes
12:03:57.681 WARN DepthPerSampleHC - Annotation will not be calculated at position chr1:817679 and possibly subsequent; genotype for sample Jagadeesh_64bit/MGH3006v2 is not called
12:03:57.681 WARN StrandBiasBySample - Annotation will not be calculated at position chr1:817679 and possibly subsequent; genotype for sample Jagadeesh_64bit/MGH3006v2 is not called
12:03:57.682 WARN DepthPerSampleHC - Annotation will not be calculated at position chr1:817681 and possibly subsequent; genotype for sample Jagadeesh_64bit/MGH3006v2 is not called
12:03:57.682 WARN StrandBiasBySample - Annotation will not be calculated at position chr1:817681 and possibly subsequent; genotype for sample Jagadeesh_64bit/MGH3006v2 is not called
12:04:00.723 INFO ProgressMeter - chr1:1238237 0.2 4370 26157.2
I looked up online and some people are saying these warnings are ignorable. But I'm not totally sure as the warnings also contain information with specific positions. Can someone help me identify errors in my code or my previous steps? How to get rid of these warnings? Are those ignorable? I plan to combine all GVCFs after this step so I want to make sure everything is handled correctly before I move forward. Thank you so much!
