I have a directory named cases, where I have 4 .vcf.gz files of merged vcf files of Indels and another 4 .vcf.gz files of merged vcf files of SNPs.
I want to now merge all the 4 merged indels into 1 file.
I received these 4 sets of indels and snps into 4 separate folders, and for set 1, the samples are named: S1, S2, S3....S50 For set 2, also, the samples are named: S1, S2, S3, ....S50 Similarly for set3 and set4.
when I try and merge these 4 merged indel files into one using:
~cases/$ /usr/bin/bcftools merge Indel/*indel.vcf.gz -Oz -o Indels.vcf.gz
Incorrect number of AD fields (2) at 1:878906 cannot merge
How can I solve this?