Skip to content

Instantly share code, notes, and snippets.

View dwaggott's full-sized avatar

Daryl Waggott dwaggott

3 followers · 2 following
View GitHub Profile
@dwaggott
dwaggott / tmp.vcf
Created April 15, 2016 21:57
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##pipeline_version=DVDS_v1.4.7.4
##resource_version=v1.0.13
##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -11.8399 <= x < -0.3411">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -24069.3954">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -24069.3954 <= x < -11.8399">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
@dwaggott
dwaggott / tmp.vcf
Created April 19, 2016 20:54
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##pipeline_version=DVDS_v1.4.7.4
##resource_version=v1.0.13
##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -11.8399 <= x < -0.3411">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -24069.3954">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -24069.3954 <= x < -11.8399">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
@dwaggott
dwaggott / -
Created April 19, 2016 21:11
debug-merge.tar.gz
@dwaggott
dwaggott / tmp.vcf
Created April 20, 2016 18:11
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##pipeline_version=DVDS_v1.4.7.4
##resource_version=v1.0.13
##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -11.8399 <= x < -0.3411">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -24069.3954">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -24069.3954 <= x < -11.8399">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
@dwaggott
dwaggott / test.vcf
Created May 5, 2016 00:12
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##pipeline_version=DVDS_v1.4.7.4
##resource_version=v1.0.13
##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -11.8399 <= x < -0.3411">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -24069.3954">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -24069.3954 <= x < -11.8399">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
@dwaggott
dwaggott / tmp.vcf
Created May 10, 2016 00:18
This file has been truncated, but you can view the full file.
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##pipeline_version=DVDS_v1.4.7.4
##resource_version=v1.0.13
##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -11.8399 <= x < -0.3411">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -24069.3954">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -24069.3954 <= x < -11.8399">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
@dwaggott
dwaggott / tmp.vcf
Created May 10, 2016 00:18
This file has been truncated, but you can view the full file.
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##pipeline_version=DVDS_v1.4.7.4
##resource_version=v1.0.13
##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -11.8399 <= x < -0.3411">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -24069.3954">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -24069.3954 <= x < -11.8399">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
@dwaggott
dwaggott / out2.bed
Created July 14, 2016 04:46
22 16121729 16121730 CA C . -1 -1 .
22 16123026 16123027 T G . -1 -1 .
22 16123163 16123164 C A . -1 -1 .
22 16123468 16123469 T G . -1 -1 .
22 16123792 16123793 G A . -1 -1 .
22 16136702 16136703 G A . -1 -1 .
22 16211243 16211244 G T . -1 -1 .
22 16211245 16211246 A G . -1 -1 .
22 16230081 16230082 T C . -1 -1 .
22 16242645 16242646 A G . -1 -1 .
@dwaggott
dwaggott / out2.bed
Created July 14, 2016 04:46
22 16121729 16121730 CA C . -1 -1 .
22 16123026 16123027 T G . -1 -1 .
22 16123163 16123164 C A . -1 -1 .
22 16123468 16123469 T G . -1 -1 .
22 16123792 16123793 G A . -1 -1 .
22 16136702 16136703 G A . -1 -1 .
22 16211243 16211244 G T . -1 -1 .
22 16211245 16211246 A G . -1 -1 .
22 16230081 16230082 T C . -1 -1 .
22 16242645 16242646 A G . -1 -1 .
@dwaggott
dwaggott / tmp.vcf
Created July 19, 2016 22:16
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20140131
##center=Complete Genomics
##source=CGAPipeline_2.0.2.22;CGAPipeline_2.0.4.11;CGAPipeline_2.0.4.14;CGAPipeline_2.0.4.18;cgatools_1.6.0
##source_GENOME_REFERENCE=NCBI build 37
##source_GENE_ANNOTATIONS=NCBI build 37.2
##reference=ftp://ftp.completegenomics.com/ReferenceFiles/build37.fa.bz2
##complete_genomics_european_wellderly_unrelated_sample_ids=GS000008112-ASM,GS000008113-ASM,GS000008115-ASM,GS000008116-ASM,GS000008117-ASM,GS000008120-ASM,GS000008121-ASM,GS000008138-ASM,GS000008155-ASM,GS000008156-ASM,GS000008158-ASM,GS000008159-ASM,GS000008162-ASM,GS000008163-ASM,GS000008164-ASM,GS000008165-ASM,GS000008166-ASM,GS000008167-ASM,GS000008168-ASM,GS000008170-ASM,GS000008174-ASM,GS000008175-ASM,GS000008176-ASM,GS000008177-ASM,GS000008228-ASM,GS000008229-ASM,GS000008230-ASM,GS000008231-ASM,GS000008232-ASM,GS000008233-ASM,GS000008234-ASM,GS000008235-ASM,GS000008236-ASM,GS000008237-ASM,GS000008238-ASM,GS000008240-ASM,GS000