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CNV consensus (8 of 6): Changing Step3 to use Bedtools Subtract #430

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merged 13 commits into from
Jan 14, 2020
Merged

CNV consensus (8 of 6): Changing Step3 to use Bedtools Subtract #430

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3f55855
add to Snakefile
Dec 18, 2019
9a923a3
resolve conflict
Dec 19, 2019
d38289c
Merge remote-tracking branch 'upstream/master'
Jan 4, 2020
3a20aa0
updating fork
Jan 4, 2020
d3d6431
Merge remote-tracking branch 'upstream/master'
Jan 6, 2020
305bbbf
changed output path and name
Jan 6, 2020
eec2ffc
update Snakefile to master
Jan 10, 2020
8f3e136
add bedtools subtract and new result file
Jan 13, 2020
bad5118
Merge branch 'master' into fix_step3
nhatduongnn Jan 13, 2020
e4c19d8
Update analyses/copy_number_consensus_call/Snakefile
nhatduongnn Jan 13, 2020
20f3278
removed get_rid_badsegment.py
Jan 13, 2020
da01485
Merge branch 'fix_step3' of https://github.com/fingerfen/OpenPBTA-ana…
Jan 13, 2020
8c25fc7
Merge branch 'master' into fix_step3
jaclyn-taroni Jan 14, 2020
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6 changes: 3 additions & 3 deletions analyses/copy_number_consensus_call/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -94,16 +94,15 @@ rule manta_filter:
rule filter_telomeres:
input:
## Define the location of the input file and take the path/extension from the config file
script=os.path.join(config["scripts"], "get_rid_bad_segments.py"),
bad_list=os.path.join(config["scripts"], "bad_chromosomal_seg_updated_merged.bed"),
bedfile="../../scratch/interim/{sample}.{caller}.{dupdel}.bed"
output:
## Define the output files' names
filtered_bed="../../scratch/interim/{sample}.{caller}.{dupdel}.filtered.bed"
threads: 1
shell:
## Invoke the python3 script and pass in the reference and CNVs files. Direct the stdout to a new file.
"python3 {input.script} --reference {input.bad_list} --file {input.bedfile} > {output.filtered_bed}"
## Invoke the bedtools subtract pass in the reference and CNVs files. Direct the stdout to a new file.
"bedtools subtract -N -a {input.bedfile} -b {input.bad_list} -f 0.5 > {output.filtered_bed}"


rule first_merge:
Expand Down Expand Up @@ -204,3 +203,4 @@ rule clean_output:
"results/cnv_consensus.tsv"
shell:
"python3 {input.script} --file {input.cnv_file} > {output}"

2 changes: 1 addition & 1 deletion analyses/copy_number_consensus_call/results/cnv_consensus.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -3167,7 +3167,7 @@ chr3 84952630 87955725 NULL 84950794:86911163:3,86911164:88297478:3 84952630:861
chr3 93649137 162808158 NULL 93649137:144671157:3,144671158:148925621:3,148925622:162808158:3 93512945:94627725:3,94627725:94631200:3,94631200:94770200:3,94770895:96420825:3,96421520:96702995:3,96702995:96706470:3,96706470:98244505:3,98244505:98249370:3,98249370:99072250:3,99072250:99227235:3,99227235:99343995:3,99343995:99347470:3,99347470:100430280:3,100430280:100435145:3,100435145:100795850:3,100795850:100827820:3,100827820:102084380:3,102085075:102991355:3,102991355:103832305:3,103833000:103955320:3,103955320:103981730:3,103981730:104394560:3,104395950:104569005:3,104569005:105774830:3,105775525:106378090:3,106378785:108032885:3,108034970:108318530:3,108319225:109156005:3,109156005:109263730:3,109266510:110058810:3,110058810:110062980:3,110062980:110371560:3,110371560:110794815:3,110796900:111147875:3,111147875:111152740:3,111152740:111361240:3,111361240:111872760:3,111872760:112468375:3,112471155:112716490:3,112717880:114292055:3,114292055:115048910:3,115048910:115053775:3,115053775:116300605:3,116301995:116589030:3,116589725:118575340:3,118575340:118686540:3,118689320:119395440:3,119395440:119533745:3,119535135:120095305:3,120095305:120916795:3,120917490:121556195:3,121556195:121561060:3,121561060:123653705:3,123653705:123659265:3,123659265:124059585:3,124061670:124968645:3,124968645:125040230:3,125040925:125204250:3,125204250:125414835:3,125414835:125418310:3,125418310:125664340:3,125871450:126530310:3,126530310:126677650:3,126677650:126696415:3,126696415:126969550:3,126970245:127350410:3,127350410:129039260:3,129041345:129350620:3,129357570:129583445:3,129584140:130044925:3,130079675:130387560:3,130388950:134391455:3,134391455:134415085:3,134415085:135905165:3,135905165:136818395:3,136818395:136947665:3,136947665:136952530:3,136952530:137153385:3,137153385:137185355:3,137185355:137791395:3,137792090:138124995:3,138125690:138409945:3,138411335:139671370:3,139672065:139769365:3,139769365:141656290:3,141656290:142283875:3,142283875:142694620:3,142694620:142698790:3,142698790:144671895:3,144671895:145747755:3,145750535:146042435:3,146042435:146230780:3,146232170:146367695:3,146367695:148630615:3,148630615:148637565:3,148638260:148773090:3,148773090:153836165:3,153836860:154109995:3,154116945:156622420:3,156622420:157090155:3,157092935:158107635:3,158108330:158594830:3,158594830:159205040:3,159205040:159214075:3,159214075:159437865:3,159437865:159444815:3,159444815:162351305:3,162352000:162447910:3,162447910:162512545:3,162512545:164365415:3,164365415:164475920:3,164477310:164801875:3,164803265:165132695:3,165132695:166291955:3,166294735:166587330:3,166587330:166592890:3,166592890:167084255:3,167084255:167358085:3,167359475:171863770:3,171863770:171867245:3 DUP BS_WY5KYSHJ
chr3 171969410 195966153 NULL 162827473:195616354:3,195616355:195730092:5,195730093:195966153:3 171969410:172147330:3,172252970:172281465:3,172281465:173296860:3,173297555:173729150:3,173729150:175556305:3,175557695:175720325:3,175723105:176335400:3,176344435:184803280:3,184805365:185514960:3,185514960:186474060:3,186474755:186773605:3,186773605:188897525:3,188903085:189042780:3,189043475:189265180:3,189270045:189441710:3,189442405:190349380:3,190352160:190477260:3,190477260:190483515:3,190483515:191922165:3,191922860:192849295:3,192850685:193417110:3,193418500:194543705:3,194544400:195148355:3,195151135:195247045:3,195247045:196596040:3,196596735:198156315:3 DUP BS_WY5KYSHJ
chr1 18423247 18601943 18422714:18428084:NA,18427821:18601943:NA 18423247:18602345:3 NULL DUP BS_X1DSETVE
chr1 149743647 207527447 147699786:224374617:NA,151192918:224378395:NA,154279508:156053291:NA,154283619:156050650:NA,154283619:156053365:NA,156051660:156078863:NA,186958658:189414983:NA,223721204:223740662:NA 149743647:151178440:3,151178441:151392366:3,151392367:152147573:3,152147574:152217223:3,152217224:152351549:3,152351550:152361499:3,152361500:153302771:3,154767417:155000246:3,155079848:155216162:3,155662919:169254659:3,169277545:206163298:3,206409065:207527447:3 NULL DUP BS_X1DSETVE
chr1 149743647 207527447 147699786:224374617:NA,151192918:224378395:NA,154279508:156053291:NA,154283619:156053365:NA,154283619:156050650:NA,156051660:156078863:NA,186958658:189414983:NA,223721204:223740662:NA 149743647:151178440:3,151178441:151392366:3,151392367:152147573:3,152147574:152217223:3,152217224:152351549:3,152351550:152361499:3,152361500:153302771:3,154767417:155000246:3,155079848:155216162:3,155662919:169254659:3,169277545:206163298:3,206409065:207527447:3 NULL DUP BS_X1DSETVE
chr2 162345760 162382530 162345760:162382854:NA 162345716:162382530:3 NULL DUP BS_X1DSETVE
chr20 15789213 15802607 15789213:15803019:NA 15788678:15802607:3 NULL DUP BS_X1DSETVE
chr20 38794600 38805566 38794600:38805943:NA 38791637:38805566:3 NULL DUP BS_X1DSETVE
Expand Down
126 changes: 0 additions & 126 deletions analyses/copy_number_consensus_call/src/scripts/get_rid_bad_segments.py
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