Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
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6.6 years ago

Hi

I am trying to add ancestral allele to 1000 Genomes Phase3 VCF files. I have used the "human_ancestor_GRCh37_e59.tar.bz2" files for ancestral allele input file. The steps I have used are:

cat human_ancestor_3.fa | sed 's,^>.*,>1,' | bgzip -c > human_ancestor_3.fa.bz

samtools faidx human_ancestor_3.fa.bz

Then using vcf-sort, sorted the chr3.vcf.gz file After that,

zcat sort.chr3.vcf.gz | fill-aa -a human_ancestor_3.fa.bz | bgzip-c>out.sort.chr3.vcf.gz

but it is giving the folllowing ERROR message:

[W::fai_fetch] Reference 3:60069-160069 not found in FASTA file, returning empty sequence Failed to fetch sequence in >3:60069-160069 The command "samtools faidx human_ancestor_3.fa.bz 3\:60069-160069" returned non-zero status 256.>3:60069-160069 at /usr/local/share/perl5/FaSlice.pm line 56. FaSlice::throw('FaSlice=HASH(0x1899f88)', 'The command "samtools faidx h uman_ancestor_3.fa.bz 3\:60069...', '.\x{a}', '>3:60069-160069\x{a}') called a t /usr/local/share/perl5/FaSlice.pm line 79 FaSlice::cmd('FaSlice=HASH(0x1899f88)', 'samtools faidx human_ancestor_3 .fa.bz 3\:60069-160069') called at /usr/local/share/perl5/FaSlice.pm line 125 FaSlice::read_chunk('FaSlice=HASH(0x1899f88)', 3, 60069) called at /usr/ local/share/perl5/FaSlice.pm line 153 FaSlice::get_base('FaSlice=HASH(0x1899f88)', 3, 60069) called at /usr/lo cal/bin/fill-aa line 148 main::fill_aa('HASH(0x13c4a68)', 'human_ancestor_3.fa.bz') called at /us r/local/bin/fill-aa line 18

Please help.

vcftools samtools faidx tabix 1000Genomes • 2.4k views
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Hello, shrutishreyajha, I met the same problem, do you fix this bug, would you share the key point with me Thanks

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This was written almost 6 years ago. You should open a new issue. Post the chromosome names in your files whether if they have prefix chr or not.

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