Commits · 741269e63078014763b4fac7cf34f1504115092a · LBMC / Delattre / JU28_59vs17_SNP · GitLab

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Oct 11, 2018
- 1_JU28_59vs17_SNP_calling.sh: add PSMN cmd · 741269e6
  Laurent Modolo authored 6 years ago
  
  741269e6
- SNP_calling.config: add bioawk for sge · ea17baf9
  Laurent Modolo authored 6 years ago
  
  ea17baf9
Oct 10, 2018
- SNP_calling.config: rename some module to load · ec7d1b21
  Laurent Modolo authored 6 years ago
  
  Unverified
  
  ec7d1b21
- SNP_calling.nf: add SGE config · 3d210a36
  Laurent Modolo authored 6 years ago
  
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  3d210a36
Oct 09, 2018
- 1_JU28_59vs17_SNP_calling.sh: test of blast · 5d990d32
  Laurent Modolo authored 6 years ago
  
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  5d990d32
- SNP_calling.nf: cleanup gatk code · b85258ad
  Laurent Modolo authored 6 years ago
  
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  b85258ad
- 1_JU28_59vs17_SNP_calling.sh: blast of 5S on the assembly · b6551f07
  Laurent Modolo authored 6 years ago
  
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  b6551f07
- intersect_SNP.R: add enzyme selection · f0432019
  Laurent Modolo authored 6 years ago
  
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  f0432019
Oct 08, 2018
- SNP_calling.nf: fix format · 16f01d2f
  Laurent Modolo authored 6 years ago
  
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  16f01d2f
- bcftools: add docker file and rm from SAMtools · 12be019b
  Laurent Modolo authored 6 years ago
  
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  12be019b
- 1_JU28_59vs17_SNP_calling.R: add SNP alert · a79c7a67
  Laurent Modolo authored 6 years ago
  
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  a79c7a67
- intersect_SNP.R: remove print · af6eda55
  Laurent Modolo authored 6 years ago
  
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  af6eda55
- intersect_SNP.R: sort results by AF · df87f670
  Laurent Modolo authored 6 years ago
  
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  df87f670
- 1_JU28_59vs17_SNP_calling.R: add SNP filtering step · 7bf6ea38
  Laurent Modolo authored 6 years ago
  
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  7bf6ea38
- SNP_calling.nf: fix missing report for samtools SNP · 8891d227
  Laurent Modolo authored 6 years ago
  
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  8891d227
- intersect_SNP.R: add restriction sequence · 120cb2a7
  Laurent Modolo authored 6 years ago
  
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  120cb2a7
- SNP_calling: add vcf to csv conversion step · f7ba71e6
  Laurent Modolo authored 6 years ago
  
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  f7ba71e6
- intersect_SNP.R: small script to return SNP in arg2 not found in arg1 · 61f2438d
  Laurent Modolo authored 6 years ago
  
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  61f2438d
- SNP_calling.nf: add SNP calling with bcftools · c72c554d
  Laurent Modolo authored 6 years ago
  
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  c72c554d
- SAMTools: add bcftools to the docker image · 5d5e3b7c
  Laurent Modolo authored 6 years ago
  
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  5d5e3b7c
Oct 06, 2018
- Bowtie2: add sambamba and samblaster to docker · 6d1694c1
  Laurent Modolo authored 6 years ago
  
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  6d1694c1
- SNP_calling.nf: change RG tag order · e5648eb2
  Laurent Modolo authored 6 years ago
  
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  e5648eb2
Oct 05, 2018
- SNP_calling.nf: add sample_name info for mapping_fastq · 533fa476
  Laurent Modolo authored 6 years ago
  
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  533fa476
- SNP_calling.nf: add RG info in bowtie22 · b5b15822
  Laurent Modolo authored 6 years ago
  
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  b5b15822
- SNP_calling.nf: change cpus number for bowtie · 2555926a
  Laurent Modolo authored 6 years ago
  
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  2555926a
- Merge branch 'bwamem' · f48326c5
  Laurent Modolo authored 6 years ago
  
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  f48326c5
- SNP_calling.nf: working pipeline with BWA MEM · 40a19885
  Laurent Modolo authored 6 years ago
  
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  40a19885
- SNP_calling.nf: add SNP_filter step · 36fafd89
  Laurent Modolo authored 6 years ago
  
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  36fafd89
Oct 04, 2018
- 1_JU28_59vs17_SNP_calling.nf: fix encoding problem for genome · 58e36e9e
  Laurent Modolo authored 6 years ago
  
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  58e36e9e
- Bioawk: add docker files · 3bc9cac1
  Laurent Modolo authored 6 years ago
  
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  3bc9cac1
Oct 03, 2018
- 1_JU28_59vs17_SNP_calling.sh: fix tests cmd · 147563d6
  Laurent Modolo authored 6 years ago
  
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  147563d6
- SNP_calling.nf: fix Mutect2 variables · d8a29f60
  Laurent Modolo authored 6 years ago
  
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  d8a29f60
- SNP_calling.nf: fix collect problem · 7619538a
  Laurent Modolo authored 6 years ago
  
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  7619538a
- SNP_calling: test with Bowtie2 · 25be4607
  Laurent Modolo authored 6 years ago
  
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  25be4607
- SNP_calling.nf: last test with BWA MEM · c9fc9da5
  Laurent Modolo authored 6 years ago
  
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  c9fc9da5
Oct 02, 2018
- BWA: add sambamba and samblaster to docker · 45be00ec
  Laurent Modolo authored 6 years ago
  
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  45be00ec
- 1_JU28_59vs17_SNP_calling.sh: add training step analysis · 6ff24e84
  Laurent Modolo authored 6 years ago
  
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  6ff24e84
Sep 26, 2018
- SNP_calling.nf: fix merge_bam · b649d2bd
  Laurent Modolo authored 6 years ago
  
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  b649d2bd
Sep 25, 2018
- SNP_calling.nf: add merging step into tumor_sample and normal_sample · 60a814b3
  Laurent Modolo authored 6 years ago
  
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  60a814b3
- SNP_calling.nf: sambamba change tmp dir · 209416f2
  Laurent Modolo authored 6 years ago
  
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  209416f2