Entering edit mode
3.2 years ago
raalsuwaidi
▴
100
Hi all,
i am trying to use IMPUTE2 with 2 reference panels to be merged. i am applying the code as per the example provided on IMPUTE2 page. but somehow the merged reference panel doesnt get produced (the REF file as per the example). any ideas?
for simplicity i am putting the code
impute2 -merge_ref_panels \
-m genetic_map_chr1_b36.txt \
-h ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.hap.gz \ local_chr1.vcf.hap.gz \
-l ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.legend.gz \
local_chr1.vcf.legend.gz \
-g fileToBeImputed.QC.CHR1.vcf.gen.gz \
-int 20.4e6 20.5e6 \
-Ne 20000 \
-merge_ref_panels_output_ref REF \
-o chrm1_output
I cant find the REF file!!!! am i doing something wrong?
What do you mean?
I mean the output from the below statement
-merge_ref_panels_output_ref REF \
You should not have any file called REF. That parameter defines the name prefix of the merged panel output files. Please see: https://mathgen.stats.ox.ac.uk/impute/panel_merging_options.html
Kevin
i changed it into -merge_ref_panels_output_ref mergedref and i still cannot see the mergedref file
Please show all status, warning, and error messages
there is no error or warning, but in the summary file the last entry is as follows:
Run log
RESETTING PARAMETERS FOR "SURROGATE FAMILY" MODELING -setting mutation matrices -setting switch rates -setting hole-filling switch rates
diploid sampling success rate: 0.000
haploid sampling success rate: (no haploid sampling performed)
i dont know what that means
If there are no warnings or errors, and the program indicates that the command was successful, then there should be output files with prefix mergedref
What output is actually produced?
these are the output files produced
imput2_combined_merged_chrm1
imput2_combined_merged_chrm1_info imput2_combined_merged_chrm1_info_by_sample imput2_combined_merged_chrm1_summary imput2_combined_merged_chrm1_warnings
the warning file is empty. and the summary file has an output of concordance value 99.5.
the code used is:
the file that should be the output of -merge_ref_panels_output_ref mergedpanel is not in the folder with the rest of the files
i have no idea what is wrong.