VCF file issue in merging

Question

[SHN]

Hello,

I started imputation with IMPUTEV2. I know it is an old version but I came this far and I would like to finish it. Now after converting the IMPUTE2 output to VCF files using SHAPEIT, I need to piece the chromosome chunks back together.

I am using bcftools in merging all the data : (my purpose is to merge all the VCF files and then import in plink file for QC and then making IBS matrix)

$BCFTOOLS merge --merge all vcf_chr1_chunk1.vcf.gz vcf_chr1_chunk2.vcf.gz vcf_chr1_chunk3.vcf.gz-O v > $results_merged_vcf'/Chromosome1.imputed.vcf

Though the program asks for the index file using

tabix -p vcf file.vcf.gz

I can not index the file as it needs to be sorted by chromosome. when I try to sort the program mention it can not parse through [--- 45000037].

In my VCF file (after converting data from IMPUTE2 output file to VCF file) I have the format below for the imputed variants.

Here is the format of my VCF file:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1610 2318 2421
--- 45000037 rs140328665:45000037:G:A G A . PASS . GT 0|0
--- 45002242 1:45002242:G:A G A . PASS . GT 0|0

So here are my questions:

1. Should I write a code in converting all the '---' to chromosome number for each chunk?

2. for the cases below:

   --- 45002242 1:45002242:G:A G A . PASS . GT 0|0

Should I manually format the second column to just the variant ID?

Should I loop over all the files and remove them, or there is a way to remove them from the beginning?

Is there any software to do this step for me for the sake of saving time?

Thank you for your help in advance

[4galaxy77]

How did you convert it from IMPUTE2 output to vcf? Seems weird that it would just discard the chromosome identifer. My suggestion would be to use a different conversion tool (plink / qctool) to convert to vcf which retains the chromosome identifier. This way you don't have to write any manual tools to do it for you.

[SHN]

I used shapeit to convert from IMPUTE2 format to VCF. There was no chromosome number from the beginning as these lines are imputed. This is the format in IMPUTE2 output format:

--- 1:35000209:G:C 35000209 G C 0 0 0

--- rs75886048:35000218:C:A 35000218 C A 1 0

--- 1:35000252:T:G 35000252 T G 0 0 0 0

and this is the output format in the VCF:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

--- 45000037 rs140328665:45000037:G:A G A . PASS . GT 0|0

--- 45002242 1:45002242:G:A G A . PASS . GT 0|0

The QCTOOLS doesn't read the '---' format and doesn't work. So you mean this VCF output is not the correct version output from shapeit2?

Thanks

Answer 1

[yeyidi9341]

Sometimes, managing multiple VCFs can be very difficult. Due to this, you should have preferred a Single VCF file with all your valuable data inside. The manual method is quite lengthy and requires technical knowledge So, so I suggest you use Merge VCF, which lets you combine multiple VCF files without any duplicates.

Visit at : https://www.wholeclear.com/merge/vcard/