ERROR: Problem opening index file for hg19.fa

[Npaffen]

shapeit4 fails to find/open the index file for the reference file hg19.fa. This file exists and is in the same folder as hg19.fa.

ls in the folder delivers the following outcome

~/Documents/GitHub/Genomics_prac_guide/reference$ ls
ALL_20141222.dbSNP142_human_GRCh38.snps.vcf.gz      hg19.fa
ALL_20141222.dbSNP142_human_GRCh38.snps.vcf.gz.csi  hg19.fa.fai
ALL_20141222.dbSNP142_human_GRCh38.snps.vcf.gz.tbi  hs37d5.fa
d5p3.re.fa.out                                      hs37d5.fa.fai
GCF_000001405.25.gz                                 hs37d5.fa.gz
GCF_000001405.25.gz.tbi                             hs37d5ss.info
GRCh38_full_analysis_set_plus_decoy_hla.dict        hs37d5ss.rep.gz
GRCh38_full_analysis_set_plus_decoy_hla.fa          hs37d5ss.repsum
h19.vcf                                             human_g1k_v37.fasta
hg19_aligned.fa                                     wget-log

shapeit4 --input /home/oem/Documents/GitHub/Genomics_prac_guide/trio/SomeName/SomeName_trio_chrMT.bcf --map /home/oem/Documents/GitHub/Genomics_prac_guide/map/genetic_map.37/chrMT.b37.gmap.gz --region MT --reference /home/oem/Documents/GitHub/Genomics_prac_guide/reference/hg19.fa --output /home/oem/Documents/GitHub/Genomics_prac_guide/trio/SomeName/SomeName_trio_chrMT_phased.bcf

I tried to manually recreate the index file using samtools faidx hg19.fa still the error persists. Does Reference VCF in the output of shapeit4 indicate that the reference file has to be in the format of vcf/bcf due to the use of HTSlib? `Files:

• Input VCF : [/home/oem/Documents/GitHub/Genomics_prac_guide/trio/SomeName/SomeName_trio_chrMT.bcf]
• Reference VCF : [/home/oem/Documents/GitHub/Genomics_prac_guide/reference/hg19.fa]
• Genetic Map : [/home/oem/Documents/GitHub/Genomics_prac_guide/map/genetic_map.37/chrMT.b37.gmap.gz]
• Output VCF : [/home/oem/Documents/GitHub/Genomics_prac_guide/trio/SomeName/SomeName_trio_chrMT_phased.bcf]`

[odelaneau]

Hi,

--reference is to specify a reference panel of haplotypes (i.e. 1000 Genomes), not the reference genome.

Best,

O

[wenyuhaokikika]

reference panel of haplotypes (i.e. 1000 Genomes),

Hello, I have encountered the same problem, how to get reference panel of haplotypes? please