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Old 06-03-2013, 06:55 AM   #1
hosang.jeon
Junior Member
 
Location: South Korea

Join Date: Jan 2012
Posts: 6
Post How to convert to or get 1000 Genomes phase1 data mapped to hg18.

Hello.

I'm trying to annotate my variant data with 1000 genomes phase1 data.
(ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf)

I need to convert above vcf file to hg18 and hg19(I think it's not so different with GRCh37).

It worked fine to convert from b37 to hg19 using liftOver.pl(gatk version).

But if I try to convert from b37 to hg18 it throws an exception with below error message.

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Badly formed variant context at location chr1:728499; getEnd() was 731936 but this VariantContext contains an END key with value 742073
##### ERROR ------------------------------------------------------------------------------------------



I've tried to change my newRef file with gatk bundle 1.2, 1.5 and 2.2.
However it throws the same error.

I've also tried to convert it from hg19 to hg18 but it throws the same error.


Is there any way to get (hg18 mapped) 1000 genomes phase1 data?
or convert to hg18?


Thanks in advance.
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Old 06-03-2013, 09:16 AM   #2
swbarnes2
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Posts: 912
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Try UCSC's LiftOver

http://genome.ucsc.edu/cgi-bin/hgLiftOver
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Old 06-03-2013, 04:46 PM   #3
hosang.jeon
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Location: South Korea

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Posts: 6
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Thank you swbarnes2.

However, the converter you let me know only can handle bed format data.
I need to convert the data of vcf format.

Even though I can convert my vcf file to bed format, it loss lots of information such as INFO, FORMAT etc.

Is there any way to handle this problem?
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Old 06-03-2013, 04:47 PM   #4
hosang.jeon
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Location: South Korea

Join Date: Jan 2012
Posts: 6
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Thank you swbarnes2.

However, the converter you let me know only can handle bed format data.
I need to convert the data of vcf format.

Even though I can convert my vcf file to bed format, it loss lots of information such as INFO, FORMAT etc.

Is there any way to handle this problem?
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Old 06-03-2013, 10:14 PM   #5
Jon_Keats
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See http://www.broadinstitute.org/gatk/g...s#Introduction

Look about half way down for lift-over
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