LDBlockShow

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Error: Line 28 of .vcf file has a GT half-call.

1

Hi! I use Plink to convert the my vcf format，but I encountered the following problems: Error: Line 28 of .vcf file has a GT half-call. Use --vcf-half-call to specify how...

Sour01

How can I close the quality check on my data?

3

Hi there, I have two genotype data in PLINK format with the same BIM file and different FAM file, now I tried to compare the LD in two dataset without...

janking1

Dose this tool need phenotypes?

1

Hello every, I conduct the commend: LDBlockShow -InVCF aln_sorted2.vcf -OutPut out -Region NC_001802.1:1:2000 -OutPng -SeleVar 2 and got the result: #Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic...

Alice-yyt

.vcf file has a GT half-call.

3

Hi, I used LDBlockShow to analysis my vcf file. But I got the following error. `Error: Line 5230 of .vcf file has a GT half-call. ` `Use --vcf-half-call to specify...

PengJia6

availability on bioconda

5

Thanks for this new tool! I found the pre-print for LDBlockShow on the biorxiv. Since LDBlockShow is distributed under an open license (MIT), I added a package recipe so it...

tomkinsc

LD - across all chroms

1

Hello, I've recently discovered this tool, and want to try it out on a large vcf. I was wondering, is there any way to get LD analysis + plot across...

siv-n

non-human genome

1

Hello, When use LDBlockShow to non-human genome, how to set the chromosome set? Thanks in avance! C

chengroup

comparing D' scores of PLINK and LDBlockShow

1

Thanks for making and sharing this great tool. I am trying to reproduce with plink the exact same D' prime values as observed in the TriangleV.gz file, using the following...

mennodejong1986

About the size of the labels x and y axis

1

Hello, I have not find size options related to labels, how can I edit or add font size codes? Thanks

pbreeder

Some sites were deleted

3

 Hi, I found some SNP/Indel sites were filtered, can I rescue them by certain parameters? And I want to calculate LD of rare variants, setting "-MAF 0", but this...

tydcg