• Dbsnp Download

Import this dataset into selected histories Download this dataset Show items using this dataset's disk file. Uploaded by: paolo.uva@crs4.it. At the '/bundle/2.8/b37' directory, use 'get dbsnp_138.b37.vcf.gz' to download the latest database of known polymorphic sites to the current local working directory.

. 140 wrote: VCF is a very flexible format & I would be careful converting Complete Genomics directly into VCF on your own - for example Complete handles complex variants very differently compared to how 1000G handled them in the Pilot phase.

Digging into the supplemental information on the Korean genome publication etc. Can help fill some of those extra fields. Also, the genomes you've mentioned contain Structural Variation data of various degrees of completeness - and VCF files do exist for these kinds of variants as well. By VCF file, do you mean you're interested in the format itself, or a particular kind of variant?

Got a problem? Search using the upper-right search box, e.g. Using the error message. Try the latest version of tools. Include tool and Java versions. Tell us whether you are following. Include relevant details, e.g.

Platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc. For tool errors, include the error stacktrace as well as the exact command. For format issues, include the result of running for BAMs or for VCFs. For weird results, include an illustrative example, e.g.

Attach IGV screenshots according to. For a seeming variant that is uncalled, include results of following. Did we ask for a bug report?

Then follow instructions in. Hi Everyone, Sorry for all the confusion on this topic. There are several things going on, but I'll try to clarify things a bit and hopefully help people get rolling again.

Reference Builds Genome builds have historically been a murky topic, although the state of affairs today is much better. The problem that people are having comes from a mis-labeling of the genome build on some of those reference files.

There are two major human genome builds in use: UCSC (aka HG19): identifiable by the use of 'chr' prefixes for chromosomes (ie chr2) b37 (1000 Genomes): does not use 'chr' prefixes (ie instead of chr2, it is just 2) At the Broad - we were using a pre-release of b37 plus extensions as our reference before UCSC/HG19 was available. Thus internally we use 'BroadHG19' which is really what became b37. Unfortunately, this creates a lot of confusion So if you want to run with b37, you should use the following files: REFERENCE: humang1kv37.fasta DBSNP: dbsnp137.b37.vcf COSMIC: b37cosmicv54120711.vcf (I just renamed this file on the download site from hg19cosmicv54120711.vcf to be more accurate) And if you want to use UCSC/HG19, you should use: REFERENCE: ucsc.hg19.fasta DBSNP: dbsnp137.hg19.vcf COSMIC: To create that COSMIC file, you should be able to use a tool like 'LiftoverVariants' from the GATK to create that. I'll also create one and post it on the download site.

Newer Versions of dbSNP and COSMIC VCFs Now that the reference build question is hopefully addressed, the second point I believe in the above is where people can obtain newer versions of these VCFs. For dbSNP, the GATK Reference Bundles contain the latest dbSNP files which MuTect can use directly. For COSMIC however, it's more problematic as COSMIC doesn't release a VCF version (that I'm aware of, but please correct me if that's not right).

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Maintaining a converter for an external data source is something that we can't support right now so it doesn't get upgraded that frequently. However, the main purpose of the COSMIC VCF is rather slight.

Sites in the COSMIC are used to do two things:. Sites that are in dbSNP and COSMIC do NOT use the prior as a site being germline during somatic classification. This is because dbSNP contains a number of sites that are common somatic events which were deposited into dbSNP in the past. We want to counteract this effect and not make these sites harder to call. Sites in COSMIC are exempt from the 'Panel of Normals' filter - again these are typically recurrent events and this is a mechanism to bypass this filter if necessary. Sites in the output callstats file are annotated as 'COSMIC' That's all - so if someone is aware of a standardized VCF for COSMIC, I'd be happy to start supporting that directly.

I used grep/sed to change the file (adding 'chr' to the beginning of non-comment lines), and it seems to work fine now. I do get a warning with the edited dbsnp file though: INFO 10:46:38,842 RMDTrackBuilder - Creating Tribble index in memory for file dbsnp132b37.leftAlignednew.vcf WARN 10:46:38,858 VCFStandardHeaderLines$Standards - Repairing standard header line for field AF because - count types disagree; header has UNBOUNDED but standard is A - descriptions disagree; header has 'Allele Frequency' but standard is 'Allele Frequency, for each ALT allele, in the same order as listed'.

Said: I'm getting the same error, using the same files as furgason5. It seems that the cosmic and dbsnp files posted don't have the 'chr' prefix for the chromosome names? I think kmdaily is right about the chromosome names.

I suspect they should be compatible with the names used in your reference genome (it might, or it might not, use the 'chr' prefix). The 'chr' prefix is not included in the dbSNP/COSMIC files provided on the MuTect's download page. I think another source of complications could be 'X' and 'Y' chromosome names used in the dbSNP file, while '23' and '24' are used in the COSMIC file. However, if this indeed is the issue (and prefix addition/text replacement in the first column of the uncommented lines in those files could solve the problems then), I wonder whether/how these very files work for kcibul.

Hi Everyone, Sorry for all the confusion on this topic. There are several things going on, but I'll try to clarify things a bit and hopefully help people get rolling again. Reference Builds Genome builds have historically been a murky topic, although the state of affairs today is much better. The problem that people are having comes from a mis-labeling of the genome build on some of those reference files. There are two major human genome builds in use: UCSC (aka HG19): identifiable by the use of 'chr' prefixes for chromosomes (ie chr2) b37 (1000 Genomes): does not use 'chr' prefixes (ie instead of chr2, it is just 2) At the Broad - we were using a pre-release of b37 plus extensions as our reference before UCSC/HG19 was available.

Thus internally we use 'BroadHG19' which is really what became b37. Unfortunately, this creates a lot of confusion So if you want to run with b37, you should use the following files: REFERENCE: humang1kv37.fasta DBSNP: dbsnp137.b37.vcf COSMIC: b37cosmicv54120711.vcf (I just renamed this file on the download site from hg19cosmicv54120711.vcf to be more accurate) And if you want to use UCSC/HG19, you should use: REFERENCE: ucsc.hg19.fasta DBSNP: dbsnp137.hg19.vcf COSMIC: To create that COSMIC file, you should be able to use a tool like 'LiftoverVariants' from the GATK to create that. I'll also create one and post it on the download site. Newer Versions of dbSNP and COSMIC VCFs Now that the reference build question is hopefully addressed, the second point I believe in the above is where people can obtain newer versions of these VCFs. For dbSNP, the GATK Reference Bundles contain the latest dbSNP files which MuTect can use directly. For COSMIC however, it's more problematic as COSMIC doesn't release a VCF version (that I'm aware of, but please correct me if that's not right).

Maintaining a converter for an external data source is something that we can't support right now so it doesn't get upgraded that frequently. However, the main purpose of the COSMIC VCF is rather slight. Sites in the COSMIC are used to do two things:. Sites that are in dbSNP and COSMIC do NOT use the prior as a site being germline during somatic classification. This is because dbSNP contains a number of sites that are common somatic events which were deposited into dbSNP in the past.

We want to counteract this effect and not make these sites harder to call. Sites in COSMIC are exempt from the 'Panel of Normals' filter - again these are typically recurrent events and this is a mechanism to bypass this filter if necessary. Sites in the output callstats file are annotated as 'COSMIC' That's all - so if someone is aware of a standardized VCF for COSMIC, I'd be happy to start supporting that directly. Thank you, that was very helpful. I see that you recommend using the latest dbSNP collection available. If I understand correctly, dbSNP mutations not present in the COSMIC database are less likely to be called by MuTect (less likely when compared to mutations not found in the dbSNP file passed to MuTect). The GATK bundle offers also 'a version of dbSNP subsetted to only sites discovered in or before dbSNP BuildID 129, which excludes the impact of the 1000 Genomes project'.

Would it be advisable to use that dbSNP collection instead? I would recommend using the latest dbSNP, not the one that excludes the 1000 Genomes project. You're correct that at sites present in the DBSNP VCF we are slightly less powered to classify mutations (not discover them in the tumor) given the exact same depth of sequencing.

However, as we describe in the publication, in practices these differences really only come into play at very low coverage in the normal (under 20x). But say you had a dataset where the normal was covered at 10x only, and you were trying to decide what to do. If you used no DBSNP file you would make a huge number of mistakes (compared to the number of true somatic events) misclassifying true germline events as somatic. On the other hand, if you use the DBSNP file you would be less able to call true somatic mutations that occur at DBSNP positions that you would otherwise. But you would not be overwhelmed by false positives.

It's a tradeoff, but one we typically don't have to make because most of the data we come across is well over 20x in the normal. Hi Kris, I came across this tread searching for something slightly different. COSMIC now provides a VCF formatted data set: They provide two VCF files - one for coding variants and one for non-coding variants of the recent v64 release.

I'm still running into issues using them. First they weren't sorted as the GATK expected (easily fixed using their sortByRef.pl script). I then wanted to combine the two VCF files so I only had to work with a single file - but the GATK spits out an error 'there are not enough columns present in the header line'. Still trying to figure out the second issue, but wanted to pass along the link to the COSMIC vcf files. Said: Here's the command I used after modifying the header; the resulting file won't be much use to anyone else because I've modified the reference sequence.

Perl./liftOverVCF.pl -vcf b37cosmicv54120711.vcf -chain b37tohg19.chain -out hg19cosmicv54120711.vcf -newRef ucsc.hg19 -oldRef humang1kv37 -gatk /usr/local/apps/GATK/GenomeAnalysisTK-2.4-7-g5e89f01/ desmo, did you figure anything else out about the difference in the original COSMIC file and the vcf version? Could anyone explain what the difference in output is when using liftOverVCF.pl when compared to stripping just the 'chr'. For example, something like 'sed 's/chr//g' Thank you, Teja. Hi, Let me clear up a few misconceptions about what roles COSMIC and dbSNP play respectively in MuTect.

DbSNP is used to reject candidate mutations that are most probably germline because they have been observed in other people. Because the level of validation of submissions to dbSNP is low, we are not confident that things being flagged as germline or somatic are trustworthy. In contrast, COSMIC is a more highly validated resource, so it is used essentially as a whitelist to 'rescue' candidate mutations that would otherwise be rejected for being in the panel of normals and/or dbSNP. We expect that anything that is really somatic that is flagged as such in dbSNP will also be in COSMIC, so we can rely on COSMIC to rescue those sites. Does that clarify how this works? Hi and, About the cosmic vcf file for Mutect, we can now download the file CosmicCodingMuts.vcf.gz and CosmicNonCodingVariants.vcf.gz from COSMIC directly.

Dbsnp Download

Is it a good and easy way to generate the vcf just by combining these two parts? But I notice that these two parts should come from CosmicCompleteExport.tsv.gz, but the current b37cosmicv54120711.vcf was transformed from CosmicMutantExport. So, I have some confuse. Do you know the differences between them? For WGS somatic mutation detection, should I use the CompleteExport? Many thanks in advance.