Off topic:Eagle 2 - Phasing

Question

[David_emir]

Hello All,

I am working on a .vcf file with 200 samples and it looks like as follows

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SRR2098177      SRR2098178       
1       10146   .       AC    A       16738.1 VQSRTrancheINDEL99.00to99.90    .       GT:AD:DP:GQ:PL 0/1:13,53:66:99:613,0,135       0/0:44,0:44:0:0,0,635   0/0:43,0:43:0:0,0,650   0/0:29

The file hold 1 to 23 + y chromosome information. My problem is, i wanted to conduct Phasing for this vcf file which is biallelic, using Eagle2, i have used forllowing command

eagle --vcf lic.vcf.gz --geneticMapFile=genetic_map_hg19_withX.txt.gz --outPrefix test.beagleImputed_phased --vcfOutFormat=z --chrom=1 --numThreads=32

Now it throws the error as

ERROR: Invalid chromosome: Y Chromosome number must be between 1 and --chromX (= 23)

I am not sure how to tackle this issue please help. Should we phase individual chromosomes? whats the exact usage of --chrom (i tried interpreting from manual, but its not that much helpful) It would be great help to me if you guys will help me in solving this issue, i am stuck here for almost 4 days without much luck. Its frustrating :(

Thanks a lot for your kind help

Dave !