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not all sites emitted with GENOTYPE_GIVEN_ALLELES
I am running HC3.3-0 with the following options (e.g. GENOTYPE_GIVEN_ALLELES):
$java7 -Djava.io.tmpdir=tmp -Xmx3900m \ -jar $jar \ --analysis_type HaplotypeCaller \ --reference_sequence $ref \ --input_file $BAM \ --intervals $CHROM \ --dbsnp $dbSNP \ --out $out \ -stand_call_conf 0 \ -stand_emit_conf 0 \ -A Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest \ -L $allelesVCF \ -L 20:60000-70000 \ --interval_set_rule INTERSECTION \ --genotyping_mode GENOTYPE_GIVEN_ALLELES \ --alleles $allelesVCF \ --emitRefConfidence NONE \ --output_mode EMIT_ALL_SITES \
The file $allelesVCF contains these neighbouring SNPs:
20 60807 . C T 118.96 . 20 60808 . G A 46.95 . 20 61270 . A C 2870.18 . 20 61271 . T A 233.60 .
I am unable to call these neighbouring SNPs; despite reads being present in the file $BAM, which shouldn't matter anyway. I also tried adding --interval_merging OVERLAPPING_ONLY to the command line, but that didn't solve the problem. What am I doing wrong? I should probably add GATK breaker/misuser to my CV...
Thank you as always.
P.S. The CommandLineGATK documentation does not say, what the default value for --interval_merging is.
P.P.S. Iterative testing a bit slow, because HC always has to do this step:
HCMappingQualityFilter - Filtering out reads with MAPQ < 20