.gitignore

.snakemake

*.gridss.working

/conda-env
/known-variants
/reads
/truth

/reference/*.fa
/reference/*.fa.fai
/reference/*.fa.gz
/reference/*.dict
/reference/*.fa.amb
/reference/*.fa.ann
/reference/*.fa.bwt
/reference/*.fa.dict
/reference/*.fa.gridsscache
/reference/*.fa.gz.fai
/reference/*.fa.gz.gzi
/reference/*.fa.img
/reference/*.fa.pac
/reference/*.fa.sa

/reference-bias/alignment-precision-recall
/reference-bias/alignments
/reference-bias/benchmark
/reference-bias/index
/reference-bias/input
/reference-bias/msa-index
/reference-bias/panvc2
/reference-bias/panvc3
/reference-bias/reads
/reference-bias/reference-bias
/reference-bias/supporting-reads-counts

/svcalls/alignments
/svcalls/benchmark
/svcalls/gridss
/svcalls/index
/svcalls/manta
/svcalls/panvc3
/svcalls/reference-flow
/svcalls/regions/chr1_selected.bed
/svcalls/temp
/svcalls/truvari

/take-one-out-chr1/alignments
/take-one-out-chr1/benchmark
/take-one-out-chr1/gatk
/take-one-out-chr1/index
/take-one-out-chr1/input
/take-one-out-chr1/panvc2
/take-one-out-chr1/panvc3
/take-one-out-chr1/reads
/take-one-out-chr1/regions/chr1_selected.bed
/take-one-out-chr1/temp