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cnv_analysis.sh
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cnv_analysis.sh
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export bam_file=__
read_counts=${bam_file/.bam/.read_counts.tsv}
gatk PreprocessIntervals \
-R /rumi/shams/genomes/hg38/hg38.fa \
--padding 0 \
-imr OVERLAPPING_ONLY \
-O hg38.preprocessed.interval_list
gatk AnnotateIntervals \
-L hg38.preprocessed.interval_list \
-R /rumi/shams/genomes/hg38/hg38.fa \
-imr OVERLAPPING_ONLY \
-O hg38.annotated.tsv
gatk CollectReadCounts \
-L hg38.preprocessed.interval_list \
-R /rumi/shams/genomes/hg38/hg38.fa \
-imr OVERLAPPING_ONLY \
-I $bam_file \
--format TSV \
-O $read_counts
gatk FilterIntervals \
-L hg38.preprocessed.interval_list \
--annotated-intervals hg38.annotated.tsv \
-I $read_counts
-imr OVERLAPPING_ONLY \
-O hg38.sample.gc.filtered.interval_list
gatk DetermineGermlineContigPloidy \
-L hg38.sample.gc.filtered.interval_list \
--interval-merging-rule OVERLAPPING_ONLY \
-I $read_counts
--contig-ploidy-priors hg38_contig_ploidy_priors.tsv \
--output . \
--output-prefix ploidy \
--verbosity DEBUG
gatk DetermineGermlineContigPloidy \
--model cohort-23wgs-20190213-contig-ploidy-model \
-I $read_counts \
-O . \
--output-prefix ploidy-case \
--verbosity DEBUG
gatk GermlineCNVCaller \
--run-mode COHORT \
-L scatter-sm/twelve_1of2.interval_list \
-I $read_counts
--contig-ploidy-calls ploidy-calls \
--annotated-intervals twelveregions.annotated.tsv \
--interval-merging-rule OVERLAPPING_ONLY \
--output cohort24-twelve \
--output-prefix cohort24-twelve_1of2 \
--verbosity DEBUG