Tagged with #reference ordered data (rod) codecs
14 documentation articles | 0 announcements | 1 forum discussion



Created 2012-07-23 23:57:06 | Updated 2012-07-23 23:57:06 | Tags: vcfcodec gatkdocs
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A new tool has been released!

Check out the documentation at VCFCodec.


Created 2012-07-23 23:57:05 | Updated 2012-07-23 23:57:05 | Tags: vcf3codec gatkdocs
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A new tool has been released!

Check out the documentation at VCF3Codec.


Created 2012-07-23 23:56:57 | Updated 2012-07-23 23:56:57 | Tags: tablecodec gatkdocs
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A new tool has been released!

Check out the documentation at TableCodec.


Created 2012-07-23 23:56:55 | Updated 2012-07-23 23:56:55 | Tags: soapsnpcodec gatkdocs
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A new tool has been released!

Check out the documentation at SoapSNPCodec.


Created 2012-07-23 23:56:45 | Updated 2012-07-23 23:56:45 | Tags: samreadcodec gatkdocs
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A new tool has been released!

Check out the documentation at SAMReadCodec.


Created 2012-07-23 23:56:44 | Updated 2012-07-23 23:56:44 | Tags: sampileupcodec gatkdocs
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A new tool has been released!

Check out the documentation at SAMPileupCodec.


Created 2012-07-23 23:56:43 | Updated 2012-07-23 23:56:43 | Tags: refseqcodec gatkdocs
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A new tool has been released!

Check out the documentation at RefSeqCodec.


Created 2012-07-23 23:56:33 | Updated 2012-07-23 23:56:33 | Tags: rawhapmapcodec gatkdocs
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A new tool has been released!

Check out the documentation at RawHapMapCodec.


Created 2012-07-23 23:56:15 | Updated 2012-07-23 23:56:15 | Tags: millsdevinecodec gatkdocs
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A new tool has been released!

Check out the documentation at MillsDevineCodec.


Created 2012-07-23 23:56:04 | Updated 2012-07-23 23:56:04 | Tags: mafcodec gatkdocs
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A new tool has been released!

Check out the documentation at MafCodec.


Created 2012-07-23 23:55:05 | Updated 2012-07-23 23:55:05 | Tags: cgvarcodec gatkdocs
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A new tool has been released!

Check out the documentation at CGVarCodec.


Created 2012-07-23 23:55:03 | Updated 2012-07-23 23:55:03 | Tags: bedtablecodec gatkdocs
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A new tool has been released!

Check out the documentation at BedTableCodec.


Created 2012-07-23 23:55:02 | Updated 2012-07-23 23:55:02 | Tags: beaglecodec gatkdocs
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A new tool has been released!

Check out the documentation at BeagleCodec.


Created 2012-07-23 23:54:56 | Updated 2012-07-23 23:54:56 | Tags: bcf2codec gatkdocs
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A new tool has been released!

Check out the documentation at BCF2Codec.

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Created 2012-12-09 02:19:39 | Updated | Tags: gatk
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I have read this on GATK's documents:

Human sequence

If you are using human data, your reads must be aligned to one of the official b3x (e.g. b36, b37) or hg1x (e.g. hg18, hg19) references. The contig ordering in the reference you used must exactly match that of one of the official references canonical orderings. These are defined by historical karotyping of largest to smallest chromosomes, followed by the X, Y, and MT for the b3x references; the order is thus 1, 2, 3, ..., 10, 11, 12, ... 20, 21, 22, X, Y, MT. The hg1x references differ in that the chromosome names are prefixed with "chr" and chrM appears first instead of last. The GATK will detect misordered contigs (for example, lexicographically sorted) and throw an error.

that said the reference order must be: chr1, chr2, chr3, ... chr22, chrX, chrY, chrM. but after I download all the bundle in GATK's ftp, I check's reference, it's with a order of :

>chrM
>chr1
>chr2
>chr3
>chr4
>chr5
>chr6
>chr7
>chr8
>chr9
>chr10
>chr11
>chr12
>chr13
>chr14
>chr15
>chr16
>chr17
>chr18
>chr19
>chr20
>chr21
>chr22
>chrX
>chrY
...

so, is it contradictory?