Liftover for vcf.gz file
Khadija Sana
Mapping coordinates
invalid unsigned integer: "."
##fileDate=20221205
##source=PLINKv1.90
##contig=<ID=1,length=247177331>
##contig=<ID=10,length=135284979>
##contig=<ID=11,length=134445627>
##contig=<ID=12,length=132288870>
##contig=<ID=13,length=114108296>
##contig=<ID=14,length=106358709>
##contig=<ID=15,length=100216155>
##contig=<ID=16,length=88677424>
##contig=<ID=17,length=78653170>
##contig=<ID=18,length=76116153>
##contig=<ID=19,length=63779292>
##contig=<ID=2,length=242692821>
##contig=<ID=20,length=62382908>
##contig=<ID=21,length=46919232>
##contig=<ID=22,length=49524957>
##contig=<ID=3,length=199322660>
##contig=<ID=4,length=191173723>
##contig=<ID=5,length=180642522>
##contig=<ID=6,length=170761396>
##contig=<ID=7,length=158812248>
##contig=<ID=8,length=146264219>
##contig=<ID=9,length=140147761>
##contig=<ID=M,length=16394>
##contig=<ID=X,length=154582607>
##contig=<ID=XY,length=154871187>
##contig=<ID=Y,length=27108407>
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MES.1106 MES.1108 MES.1109 MES.1110 MES.1111 MES.1113 MES.1114 MES.1115 MES.1116 X1AL X2AL X4AL X5AL X7AL X9AL X11AL X13AL X15AL X16AL X17AL X18AL X19AL X20AL X21AL X22AL X23AL X24AL X25AL X26AL X27AL X28AL X29AL X30AL X31AL X32AL X33AL X34AL X35AL X36AL X37AL X38AL X39AL X40AL X41AL X42AL X43AL X44AL X45AL X46AL X47AL X48AL X49AL X50AL
X51AL X52AL X53AL X54AL X55AL X56AL X57AL X58AL X59AL X60AL X61AL X62AL X63AL X64AL X65AL X66AL X67AL X68AL X69AL X70AL X71AL X72AL X73AL X74AL X75AL X76AL X77AL
1 742429 . A G . . PR GT 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1
0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1
0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0
Luis Nassar
Hello, Khadija.
Thank you for your interest in the Genome Browser.
By default, the liftOver utility requires the files to be in BED format (http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1). It also supports GFF, but not VCF.
Additionally, the chromosome names are expected to be in 'UCSC standard', meaning 'chr1' instead of '1'.
We do offer some command line utilities to facilitate these conversions, e.g. for linux:
vcfToBed: https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/vcfToBed
chromToUcsc (converts the 1 to chr1s): https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chromToUcsc
However, another option would be crossmap which can perform better
for SNPs and supports VCF format. You can learn more about the program
from
their website, http://crossmap.sourceforge.net/. Unfortunately, we do
not maintain crossmap so I cannot provide guidance on how to use the
tool if you have any questions. They do have an active community in
BioStars, though (https://www.biostars.org/).
Also, it appears your vcf may have been created from a plink file. You may also find the following biostars question helpful: https://www.biostars.org/p/252938/
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
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