-
Notifications
You must be signed in to change notification settings - Fork 0
ICGC ARGO DNA Seq Analysis Pipeline
lindaxiang edited this page Aug 17, 2022
·
3 revisions
- GRCh38 Genome Build Version: GRCh38DH
| file name | size | md5sum |
|---|---|---|
| GRCh38_hla_decoy_ebv.fa | 3263683042 | 64b32de2fc934679c16e83a2bc072064 |
| GRCh38_hla_decoy_ebv.fa.fai | 154196 | 5ccc91e56dc4a05448dd5b9507ec6bc6 |
| GRCh38_hla_decoy_ebv.fa.gz | 918931038 | 9513ce08c458ac88f8411dcf01097a1f |
| GRCh38_hla_decoy_ebv.fa.gz.fai | 154196 | 5ccc91e56dc4a05448dd5b9507ec6bc6 |
The above files need to be staged under a path in the file system where workflow
jobs can access. The files can be downloaded using wget, one example is given as
below:
wget https://object.cancercollaboratory.org:9080/swift/v1/genomics-public-data/reference-genome/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa.fai
- This reference genome is used by the ICGC ARGO for DNA-Seq Analysis. This file is composed of the following sequences:
- GRCh38 primary assembly
- Decoy sequences
- Epstein-Barr virus (EBV) sequence
- Alternate loci scaffolds
- HLA sequences
| file name | size | md5sum |
|---|---|---|
| GRCh38_hla_decoy_ebv.dict | 480732 | eea9d8e1d3a172362f4d16de7415bd79 |
| GRCh38_hla_decoy_ebv.fa.dict | 480732 | eea9d8e1d3a172362f4d16de7415bd79 |
| GRCh38_hla_decoy_ebv.fa.fai | 154196 | 5ccc91e56dc4a05448dd5b9507ec6bc6 |
| GRCh38_hla_decoy_ebv.fa.gz.alt | 487553 | b07e65aa4425bc365141756f5c98328c |
| GRCh38_hla_decoy_ebv.fa.gz.amb | 20199 | e4dc4fdb7358198e0847106599520aa9 |
| GRCh38_hla_decoy_ebv.fa.gz.ann | 448319 | f228aeed2106bc6b0cf880317132ac2d |
| GRCh38_hla_decoy_ebv.fa.gz.bwt | 3217347004 | 7f0c8dcfc86b7c2ce3e3a54118d68fbd |
| GRCh38_hla_decoy_ebv.fa.gz.fai | 154196 | 5ccc91e56dc4a05448dd5b9507ec6bc6 |
| GRCh38_hla_decoy_ebv.fa.gz.gzi | 799928 | 11af7c4adcf5d2e211a4ed03a1a8c73e |
| GRCh38_hla_decoy_ebv.fa.gz.pac | 804336731 | 178862a79b043a2f974ef10e3877ef86 |
| GRCh38_hla_decoy_ebv.fa.gz.sa | 1608673512 | 91a5d5ed3986db8a74782e5f4519eb5f |
The above files need to be staged under a path in the file system where workflow
jobs can access. The files can be downloaded using wget, one example is given as
below:
wget https://object.cancercollaboratory.org:9080/swift/v1/genomics-public-data/reference-genome/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.dict
| file name | size | md5sum |
|---|---|---|
| CNV_SV_ref_GRCh38_hla_decoy_ebv_brass6+.tar.gz | 4257793984 | 90a100d06dbde243c6e7e11e6a764374 |
| SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment.tar.gz | 1550158859 | 03ac504f1a2c0dbe34ac359a0f8ef690 |
| VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91.tar.gz | 90122115 | 876657ce8d4a6dd69342a9467ef8aa76 |
| core_ref_GRCh38_hla_decoy_ebv.tar.gz | 899142864 | 6448a15bcc8f91271b1870a3ecfcf630 |
| qcGenotype_GRCh38_hla_decoy_ebv.tar.gz | 11472540 | 1956e28c1ff99fc877ff61e359e1020c |
The above files were originated from Sanger Reference Archives and need to be staged under a path in the file system where workflow
jobs can access. The files can be downloaded using wget, one example is given as
below:
wget https://object.cancercollaboratory.org:9080/swift/v1/genomics-public-data/sanger-variant-calling/qcGenotype_GRCh38_hla_decoy_ebv.tar.gz
| file name | size | md5sum |
|---|---|---|
| 1000g_pon.hg38.vcf.gz | 17273497 | e236330d8d156d2aad2d0930a2440177 |
| 1000g_pon.hg38.vcf.gz.tbi | 1534802 | b95230d6634c3926fb0b4f104518a0f5 |
| af-only-gnomad.hg38.vcf.gz | 3184275189 | a4209be7fb4b5a5a8d3b778132cb7401 |
| af-only-gnomad.hg38.vcf.gz.tbi | 2443190 | a7efccb1519f046c19cdf9f28559d747 |
| af-only-gnomad.pass-only.biallelic.snp.hg38.vcf.gz | 3529021364 | 6009ac7799419f69f19957a2ba1b3a16 |
| af-only-gnomad.pass-only.biallelic.snp.hg38.vcf.gz.tbi | 3121555 | 54bbff8e5637e5505eb06a0186d9b306 |
| af-only-gnomad.pass-only.hg38.vcf.gz | 4461091562 | 1c0240e5b752c8e414a86d204e4768fb |
| af-only-gnomad.pass-only.hg38.vcf.gz.tbi | 3259267 | c537795d90d71e56279545e1682f5fdf |
| small_exac_common_3.hg38.vcf.gz | 1297183 | 4c75c1755a45c64e8af7784db7fde009 |
| small_exac_common_3.hg38.vcf.gz.tbi | 242095 | f650d1dda6bd68cba65d77f131147985 |
The above files were originated from GATK Best Practices Resources and need to be staged under a path in the file system where workflow jobs can access. The files can be downloaded using wget, one example is given as below:
wget https://object.cancercollaboratory.org:9080/swift/v1/genomics-public-data/gatk-resources/1000g_pon.hg38.vcf.gz
| file name | size | md5sum |
|---|---|---|
| mutect2.scatter_by_chr/chr1.interval_list | 180 | 24d9137f7ccd5c2803d58ef56b8b3f53 |
| mutect2.scatter_by_chr/chr10.interval_list | 182 | 512975027d78247fcb19166882fd51bf |
| mutect2.scatter_by_chr/chr11.interval_list | 182 | 4e51ed603da33710c7f1b8698f79649d |
| mutect2.scatter_by_chr/chr12.interval_list | 182 | 0f29b41613170edfca43fd27073c5079 |
| mutect2.scatter_by_chr/chr13.interval_list | 182 | d4dd4925e687cc9fce124dee7b063bb2 |
| mutect2.scatter_by_chr/chr14.interval_list | 182 | 17b4b3f0e549ed5acd1d4897bf8d0100 |
| mutect2.scatter_by_chr/chr15.interval_list | 182 | 9cfd133e2e3f90e37f8097048285e927 |
| mutect2.scatter_by_chr/chr16.interval_list | 180 | 9f4b5fb8db1493214d1aa540aecfc231 |
| mutect2.scatter_by_chr/chr17.interval_list | 180 | ff20b86a75cf9f329e2b935ea4edb2d3 |
| mutect2.scatter_by_chr/chr18.interval_list | 180 | 7607a18fa2a9ef98b4548c3d19e905c4 |
| mutect2.scatter_by_chr/chr19.interval_list | 180 | 2d95d0b4dc2282215c1981f759335ff4 |
| mutect2.scatter_by_chr/chr2.interval_list | 180 | 9991a595530b6b06cafdb4ec62e6b419 |
| mutect2.scatter_by_chr/chr20.interval_list | 180 | 645342a858273248874e99acb29c50d5 |
| mutect2.scatter_by_chr/chr21.interval_list | 180 | 46907e8a00757980748c4a39864b8af5 |
| mutect2.scatter_by_chr/chr22.interval_list | 180 | fe4a33ce8693de2384ab447fb09f6f1b |
| mutect2.scatter_by_chr/chr3.interval_list | 180 | 0548550722522719b2e4f0a1c8c3de42 |
| mutect2.scatter_by_chr/chr4.interval_list | 180 | 191cdd70699c18d9fc68af035f00b0ef |
| mutect2.scatter_by_chr/chr5.interval_list | 180 | f6e3b6b42e3f020c476aa89e7cbb32fc |
| mutect2.scatter_by_chr/chr6.interval_list | 180 | e639558c71d116419dfcf41bbd2a4413 |
| mutect2.scatter_by_chr/chr7.interval_list | 180 | b166ff8931a4ef196052b7cf961e71d3 |
| mutect2.scatter_by_chr/chr8.interval_list | 180 | 86971574be70f3c6a38c8f6f8ad74f26 |
| mutect2.scatter_by_chr/chr9.interval_list | 180 | b4aa7ed56e505cf6f9b0eca9ddc8c319 |
| mutect2.scatter_by_chr/chrXY.interval_list | 358 | bfef3db07d46c8d8d5c893c3cca827f3 |
| bqsr.sequence_grouping.grch38_hla_decoy_ebv.csv | 89497 | 8ea70d26ffae94f8e14f321a7c0e7680 |
| bqsr.sequence_grouping_with_unmapped.grch38_hla_decoy_ebv.csv | 89509 | 1f6db058b2209485852059ecb69d7535 |
These files have been checked into GitHub repository
for the Mutect2 workflow. To get the files you may just clone the repo, or download using
wget using the URL pattern as in the following example:
wget https://raw.githubusercontent.com/icgc-argo/gatk-mutect2-variant-calling/main/assets/mutect2.scatter_by_chr/chr1.interval_list
| file name | size | md5sum |
|---|---|---|
| open_access.gencode_v38.20210915.bed.gz | 129538 | 6c6781661cd3bf2c3060577e597928d3 |
The file has been checked into GitHub repository for the workflow. To get the file you may just clone the repo, or download using
wget using the URL pattern as in the following example:
wget https://object.cancercollaboratory.org:9080/swift/v1/genomics-public-data/open-access-regions/open_access.gencode_v38.20210915.bed.gz