I am trying to do phasing with Eagle (Eagle v2.3.5).i Have a .vcf of 122 samples (human diseased samples). I have referred the Eagle manual but i am not able to understand --chrome function in it. I ran a command as follows:
eagle --vcf split_multiallelic.vcf.gz --geneticMapFile genetic_map_hg19_withX.txt.gz --chrom=1 --outPrefix split_multiallelic.beagleImputed.vcf.gz --vcfOutFormat=z
If i skip "--chrom" flag it throws me the following error
ERROR: File contains data for >1 chromosome; specify one with --chrom
ERROR: Invalid chromosome: Y Chromosome number must be between 1 and --chromX (= 23)
I am not able to understand this function, i have just run chrom=1, i have an VCF with multiple chromosome data what should i be doing next in this case? Will you guys help m e in understanding the function and usage of --chrom in eagle? is it obligatory to give? treat my knowledge about this topic as entry level .
Thanks a lot, its of a great help to me. Take care Dave!