Where to obtain HumanNCBI37_UCSC reference sequence?

[davecurtis]

Hi.

Please can somebody let me know where I can obtain the HumanNCBI37_UCSC reference sequence? It is hg19 but standard hg19 reference files have incompatible dictionaries compared with BAM files aligned with this reference. Please tell me where I can download this reference file from. I've looked everywhere (including both NCBI and UCSC) and can't find it. Thanks for your help.

Regards

- Dave Curtis

[GenoMax]

Hi.

Please can somebody let me know where I can obtain the HumanNCBI37_UCSC reference sequence? It is hg19 but standard hg19 reference files have incompatible dictionaries compared with BAM files aligned with this reference. Please tell me where I can download this reference file from. I've looked everywhere (including both NCBI and UCSC) and can't find it. Thanks for your help.

Regards

- Dave Curtis

What does that (bold above) mean? All Hg19 files are in this directory at UCSC: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/

[davecurtis]

Thanks. I don't see the file I am looking for in that folder.

I have a set of BAM files which have been aligned using this file:
samtoolsRefFile=/illumina/scratch/services/Genomes/FASTA_UCSC/HumanNCBI37_UCSC/HumanNCBI37_UCSC_XX.fa

I have a reference file called hg19_UCSC.fa and for most chromosomes HaplotypeCaller runs fine using this reference sequence. However with HaplotypeCaller for chromosomes 19, 21 and 22 I get this error message:
WARN 08:38:22,963 SequenceDictionaryUtils - Input files reads and reference have incompatible contigs: The following contigs included in the intervals to process have different indices in the sequence dictionaries for the reads vs. the reference: [chr22]. As a result, the GATK engine will not correctly process reads from these contigs. You should either fix the sequence dictionaries for your reads so that these contigs have the same indices as in the sequence dictionary for your reference, or exclude these contigs from your intervals. This error can be disabled via -U ALLOW_SEQ_DICT_INCOMPATIBILITY, however this is not recommended as the GATK engine will not behave correctly..

In fact, even if I set ALLOW_SEQ_DICT_INCOMPATIBILITY I still get the error and I don't get any calls for these chromosomes.

It seems that there is some incompatibility in the dictionaries of the BAM and reference files which I have not been able to fix.

Using google, I have seen other people refer to the HumanNCBI37_UCSC reference sequence so I assume it is a standard reference for hg19 but presumably with a slightly different dictionary from the file called hg19_UCSC.fa.

[GenoMax]

Perhaps someone else will have a better answer ...

You may have to ask whoever aligned those files in the first place as to where they got their reference from. With patches/releases it may be difficult to nail down an exact provenance for a file that claims to be HumanNCBI37_UCSC reference unless you know that it was obtained from the directory I posted above at UCSC.

[davecurtis]

Thanks. I think I've worked it out. The BAM files I have were prepared with two different references - one with the Y chromosome and one without and this threw out the indexing for the chromosomes listed after.