Merge pull request #677 from apeltzer/dev

Better GRCH38 Documentation for input files

Author: maxulysse

docs/REFERENCES.md

@@ -17,20 +17,57 @@ The following files need to be downloaded:
 - dd05833f18c22cc501e3e31406d140b0 - 'human\_g1k\_v37\_decoy.fasta.gz'
 - a0764a80311aee369375c5c7dda7e266 - 'Mills\_and\_1000G\_gold\_standard.indels.b37.vcf.gz'
 
-### Other files
+### Other files for GRCh37
 
 From our repo, get the [`intervals` list file](https://raw.githubusercontent.com/SciLifeLab/Sarek/master/repeats/wgs_calling_regions.grch37.list). More information about this file in the [intervals documentation](INTERVALS.md)
 
 Description of how to generate the Loci file used in the ASCAT process is described [here](https://github.com/SciLifeLab/Sarek/blob/master/docs/ASCAT.md).
 
-You can create your own cosmic reference for any human reference as specified below.
+You can create your own cosmic reference for any human reference as specified below in the Cosmic section.
 
-### COSMIC files
+## GRCh38
+
+Use `--genome GRCh38` to map against GRCh38. Before doing so and if you are not on UPPMAX, you need to adjust the settings in `genomes.config` to your needs.
+
+To get the needed files, download the GATK bundle for GRCh38 from [ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/](ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/). You can also download the required files from the Google Cloud mirror link [here](https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0).
+
+The MD5SUM of `Homo_sapiens_assembly38.fasta` included in that file is 7ff134953dcca8c8997453bbb80b6b5e.
+
+If you download the data from the FTP servers `beta/` directory, which seems to be an older version of the bundle, only `Homo_sapiens_assembly38.known_indels.vcf` is needed. Also, you can omit `dbsnp_138_` and `dbsnp_144` files as we use `dbsnp_146`. The old ones also use the wrong chromosome naming convention. The Google Cloud mirror has all data in the `v0` directory, but requires you to remove the `resources_broad_hg38_v0_` prefixes from all files.
+
+The following files need to be downloaded:
+ 
+- 3884c62eb0e53fa92459ed9bff133ae6 - 'Homo_sapiens_assembly38.dict'
+- 7ff134953dcca8c8997453bbb80b6b5e - 'Homo_sapiens_assembly38.fasta'
+- b07e65aa4425bc365141756f5c98328c - 'Homo_sapiens_assembly38.fasta.64.alt'
+- e4dc4fdb7358198e0847106599520aa9 - 'Homo_sapiens_assembly38.fasta.64.amb'
+- af611ed0bb9487fb1ba4aa1a7e7ad21c - 'Homo_sapiens_assembly38.fasta.64.ann'
+- d41d8cd98f00b204e9800998ecf8427e - 'Homo_sapiens_assembly38.fasta.64.bwt'
+- 178862a79b043a2f974ef10e3877ef86 - 'Homo_sapiens_assembly38.fasta.64.pac'
+- 91a5d5ed3986db8a74782e5f4519eb5f - 'Homo_sapiens_assembly38.fasta.64.sa'
+- f76371b113734a56cde236bc0372de0a - 'Homo_sapiens_assembly38.fasta.fai'
+- 14cc588a271951ac1806f9be895fb51f - 'Homo_sapiens_assembly38.known_indels.vcf.gz'
+- 1a55fdfa6533ae5cbc70e8188e779229 - 'Homo_sapiens_assembly38.known_indels.vcf.gz.tbi'
+- 2e02696032dcfe95ff0324f4a13508e3 - 'Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
+- 4c807e2cbe0752c0c44ac82ff3b52025 - 'Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi'
+
+If you just downloaded the `Homo_sapiens_assembly38.fasta.gz` file, you would need to do:
+
+```
+gunzip Homo_sapiens_assembly38.fasta.gz
+bwa index -6 Homo_sapiens_assembly38.fasta
+```
+
+Description of how to generate the Loci file used in the ASCAT process is described [here](https://github.com/SciLifeLab/Sarek/blob/master/docs/ASCAT.md).
 
-To annotate with COSMIC variants during MuTect1/2 Variant Calling you need to create a compatible VCF file.
+You can create your own cosmic reference for any human reference as specified below in the Cosmic section.
+
+## COSMIC files
+
+To annotate with COSMIC variants during MuTect1/2 Variant Calling you need to create a compatible VCF file. 
 Download the coding and non-coding VCF files from [COSMIC](http://cancer.sanger.ac.uk/cosmic/download) and
 process them with the [Create\_Cosmic.sh](https://github.com/SciLifeLab/Sarek/tree/master/scripts/Create_Cosmic.sh)
-script. The script requires a fasta index `.fai`, of the reference file you are using.
+script for either GRCh37 or GRCh38. The script requires a fasta index `.fai`, of the reference file you are using.
 
 Example:
 
@@ -47,23 +84,6 @@ To index the resulting VCF file use [igvtools](https://software.broadinstitute.o
 igvtools index <cosmicvxx.vcf>
 ```
 
-## GRCh38
-
-Use `--genome GRCh38` to map against GRCh38. Before doing so and if you are not on UPPMAX, you need to adjust the settings in `genomes.config` to your needs.
-
-To get the needed files, download the GATK bundle for GRCh38 from [ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/](ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/).
-
-The MD5SUM of `Homo_sapiens_assembly38.fasta` included in that file is 7ff134953dcca8c8997453bbb80b6b5e.
-
-From the `beta/` directory, which seems to be an older version of the bundle, only `Homo_sapiens_assembly38.known_indels.vcf` is needed. Also, you can omit `dbsnp_138_` and `dbsnp_144` files as we use `dbsnp_146`. The old ones also use the wrong chromosome naming convention.
-
-Afterwards, the following needs to be done:
-
-```
-gunzip Homo_sapiens_assembly38.fasta.gz
-bwa index -6 Homo_sapiens_assembly38.fasta
-```
-
 ## smallGRCh37
 
 Use `--genome smallGRCh37` to map against a small reference genome based on GRCh37. `smallGRCh37` is the default genome for the testing profile (`-profile testing`).