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HaplotypeCaller can't call a 10bp deletion variant
Hi, GATK team.
I use haplotypeCaller to call variants, but it can't find a 10bp deletion variant, as you can see in the graph.
I use -L targetInterval
to see whether haplotype is correctly assembled, but the haplotype.bam is empty, it seems the targetInterval is not active region.
Then I use -forceActive, the haplotype.bam is not empty anymore, but the output vcf file still doesn't contain the 10bp deletion variant, so I'm really confused now, what should I do to call this variant out.
I use gatk3.6.
the 10 bp deletion's position is chr17:29541466.
Here is my pipeline:
java -d64 -server -XX:+UseParallelGC -XX:ParallelGCThreads=2 -Djava.io.tmpdir=$tmp_dir -jar $gatk \
-R $reference_file \
-L 17:29,541,000-29,542,000 \
-bamWriterType ALL_POSSIBLE_HAPLOTYPES \
-T HaplotypeCaller \
-I $in_dir/NA12878MOD_sort_markdup_vardict_sort_realign_recal.bam \
--dbsnp $dbsnp_del100 \