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FindCoveredIntervals -minBQ -minMQ -cov
When running FindCoveredIntervals for GATK version 3.3-0:
java -Xmx20g -jar GenomeAnalysisTK.jar -T FindCoveredIntervals -R Homo_sapiens_assembly19.fasta -I s_C_000036_T001_d.bam -minBQ 20 -minMQ 20 -cov 20 -o s_C_000036_T001_d.list -rf FailsVendorQualityCheck -rf BadMate -rf UnmappedRead -rf BadCigar
When we open the interval in IGV (file attached) you can observe that the coverage at the start and end of the interval is lower than the set threshold of 20.
If you don't mind explaining as to why that would be the case and how can we get intervals that are satisfy the above criteria that will be great.