phasing with Eagle

Question

[David_emir]

Hi All,

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

and

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!

[WouterDeCoster]

https://data.broadinstitute.org/alkesgroup/Eagle/

If your target VCF/BCF file contains data from multiple chromosomes, you must specify one chromosome to phase using the --chrom option.

I'd suggest splitting your file per chromosome, phasing the parts, recombining the results.

[David_emir]

Thanks a lot For replying, can you please let me know the best possible way to split a file. Please treat my knowledge about this as a beginner .Should i split files for all the chromosome and run phasing on it? Individually? please let me know the best possible way for it. Thanks a lot for your kind help

[WouterDeCoster]

Googling "Split vcf by chromosome" will give you plenty of suggestions on how to generate a VCF file per chromosome.