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SVDiscovery yielding far greater than expected number of polymorphic sites

Hi Bob,

I ran SVPreprocess and SVDiscovery on a couple of loci in the human genome, each about 2 Mb in size, using high-coverage WGS data from 200 samples aligned to hg38 as input. One locus has multiple paralogous genes within it whereas the other does not. The SVDiscovery yielded ~4000 variants in each of the two loci which seems like an excessive number of variants given the size of these loci. Of these, one locus had 6 variants for which the filter status was "PASS" and the other had 35. I kept the minimum size for SV deletion discovery at default (100 bp), so this seems unlikely to be explained by SNVs or indels. Would be great to get your thoughts on why this might be happening.

Below are the scripts that I ran:

SVPreprocess

java -Xmx4g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R path_to_rmd_dir/reference_genome.fasta/Homo_sapiens_assembly38.fasta \
-I input_bam_files.list \
-md ${runDir}/metadata \
-L chr*:***-*** \
-jobLogDir ${runDir}/logs \
-run

SVDiscovery

java -Xmx4g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVGenotyper.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R path_to_rmd_dir/reference_genome.fasta/Homo_sapiens_assembly38.fasta \
-I input_bam_files.list \
-genderMapFile gender_map_file.txt \
-md ${runDir}/metadata \
-L chr*:***-*** \
-runDirectory run1 \
-jobLogDir run1/logs \
-O run1/svdiscovery.dels.vcf \
-minimumSize 100 \
-maximumSize 100000 \
-run

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