How to deal with the Error messages using hap.py with VFC in example catalogue

[GeorgeBGM]

Hi,Peter I want to compare two VCF file using hap.py, So I try to test hap.py as document described, ,But I got serval error messages like below,Can you give me several advises. ################ The code I used################# hap.py -r /home/users/ddu/software/Genome10X/hap.py/example/happy/hg38.chr21.fa PG_NA12878_chr21.vcf.gz NA12878_chr21.vcf.gz -f PG_Conf_chr21.bed.gz -o test --keep-scratch ################ The error messages###############
As for the error messages above, such as "Preprocess command preprocess /tmp/tmpc_Pztk.vcf.gz:* -l chr21:46758486-2147483647 -o /tmp/input.chr21:46758486-2147483647xS7SHk.prep.vcf.gz -V 1 -L 1 -r /example/happy/hg38.chr21.fa failed." I found there doesn't exists /tmp/tmpc_Pztk.vcf.gz:* file, so what should I do to avoid this error message using default test data. what's more, Is there need any preprocess to filter my own VCF file before using hap.py? The file in "example/happy/*gz" can be a template or not? Thanks,I am looking forwards to your reply. Best, Duo

[GeorgeBGM]

Hi,Peter I'm still confused with using hap.py to judge the Haplotype of two VCF file,I'm wondering if this situation will be considered the same, which is displayed the follow. ################################################### A VCF file: chr1 28904965 . C T 0|1 chr1 28904967 . C T 1|0 B VCF file: chr1 28904965 . C T 1|0 chr1 28904967 . C T 0|1 #################################################### Thanks,I am looking forwards to your reply. Best, Duo