Question: Locus Zoom Issuing "No valid markers in VCF file" on a VCF created in Plink 1.9
0
gravatar for Vincent Laufer
2.9 years ago by
Vincent Laufer1.0k
United States
Vincent Laufer1.0k wrote:

What follows is output from locus zoom followed by a sample of the first 20 lines and first 12 columns of a vcf file. The vcf file is bgzipped and tabixed. It was created directly from plink1.9.

I'm receiving the message "Error: no valid markers in VCF file to compute LD from.."

I am writing to ask if anyone has encountered a similar problem while using either locuszoom or plink1.9. I have not contacted the authors of locuszoom because in the past I never received a response to another query. Any help would be much appreciated.

LZ output:

Using /share/apps/ngs-ccts/locuszoom/locuszoom-1.3/bin/locuszoom.R..

Beginning plotting sequence for: chr5_7512611-8512611

Extracting region of interest (chr5:7512611-8512611) from input file..

Attempting to find best SNP in region..

Found: chr5:8012611

Using user-specified VCF file to calculate LD with reference SNP chr5:8012611..

Error: no valid markers in VCF file to compute LD from..

Grabbing annotations from SQLite database..

Creating plot..

Warning message:

No usable LD information.

Deleting temporary files..

Time required: 0d:0h:0m:35s

command used to display file: zcat MTRR_area_ra_susc.vcf.gz | head -20 | awk '{print $1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12}'

output of command ##fileformat=VCFv4.2
##fileDate=20160531
##source=PLINKv1.90
##contig=<id=5,length=9999893>
##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 0_1501_1 1_1502_1 2_1503_1

5 6000051 rs17818165 C T . . PR GT 0/1 0/0 0/0

5 6000064 rs466640 A T . . PR GT 0/1 0/0 0/1

5 6000282 rs7718138 C T . . PR GT 0/0 0/0 0/0

5 6000403 rs823742 T C . . PR GT 0/1 0/0 0/1

5 6000494 rs823743 C T . . PR GT 0/1 0/0 0/1

5 6000584 rs258972 G A . . PR GT 0/0 0/0 0/1

5 6000847 rs823568 C T . . PR GT 0/1 0/0 0/1

5 6001581 rs466015 A G . . PR GT 0/1 0/0 0/1

5 6001813 rs460967 C G . . PR GT 0/1 0/0 0/1

5 6001868 rs461940 A G . . PR GT 0/1 0/0 0/1

5 6001992 rs464210 A T . . PR GT 0/1 0/0 0/1

5 6002069 rs435787 G T . . PR GT 0/1 1/1 0/1

5 6002085 rs258971 C G . . PR GT 0/0 0/0 0/0

The actual VCF file is tab-delimited, the quick and dirty awk command is why it becomes single space delimited. Has anyone dealt with an issue like this?

locuszoom plink2 vcf • 1.3k views
ADD COMMENTlink modified 25 days ago by clisun0 • written 2.9 years ago by Vincent Laufer1.0k
0
gravatar for chrchang523
2.9 years ago by
chrchang5234.9k
United States
chrchang5234.9k wrote:

First thing I'd try is converting the spaces back to tabs, since the VCF format is explicitly defined to be tab-delimited. "cat [space-delimited VCF filename] | tr ' ' '\t' > [new VCF filename]" should do the trick.

ADD COMMENTlink written 2.9 years ago by chrchang5234.9k

Hi Chris!

Thanks very much for your reply.

The VCF file is tab-delimited. The post I posted here is space delimited, due to the awk line that I used to display it here for people to look at. What I was trying to say is that the single-spacing is not an issue, because the VCF file is correctly formatted, despite the way I reprinted here.

Sorry for any confusion that caused.

What would you try next?

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Vincent Laufer1.0k

The LocusZoom documentation states that a tabix index is required for the VCF file; do you have that?

Next thing I'd try after that is phasing the calls.

ADD REPLYlink written 2.9 years ago by chrchang5234.9k

yes, the file is tabix indexed. why would phasing be necessary if the metric being used is r^2 and not D prime?

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Vincent Laufer1.0k
0
gravatar for clisun
25 days ago by
clisun0
clisun0 wrote:

Hello, Laufer I have the same issue. Did you solve the problem Thanks Charlie

ADD COMMENTlink written 25 days ago by clisun0

If you type "plink --version" for the version of plink that generated the VCF, what do you get?

ADD REPLYlink written 25 days ago by chrchang5234.9k
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