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Old 10-13-2017, 12:23 AM   #14
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Location: India

Join Date: Oct 2017
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Default Error in Last step

Originally Posted by Petr View Post

I've just extended the documentation of fill-aa to answer this frequently asked question:

About: This script fills ancestral alleles into INFO column of VCF files. It depends on samtools, therefore the fasta sequence must be gzipped (not bgzipped!) and indexed by samtools faidx. The AA files can be downloaded from
and processed as shown in the example below. This is because the sequences in the original files are named as 'ANCESTOR_for_chromosome:NCBI36:1:1:247249719', but the underlying requires names as 'chr1' or '1'.

# Get the files ready: compress by gzip and index by samtools faidx. Either repeat the
# following command for each file manually
bzcat human_ancestor_1.fa.bz2 | sed 's,^>.*,>1,' | gzip -c > human_ancestor_1.fa.gz
samtools faidx human_ancestor_1.fa.gz

# .. or use this loop (tested in bash shell)
ls human_ancestor_*.fa.bz2 | while read IN; do
OUT=`echo $IN | sed 's,bz2$,gz,'`
CHR=`echo $IN | sed 's,human_ancestor_,, ; s,.fa.bz2,,'`
bzcat $IN | sed "s,^>.*,>$CHR," | gzip -c > $OUT
samtools faidx $OUT

# After this has been done, the following command should return 'TACGTGGcTGCTCTCACACAT'
samtools faidx human_ancestor_1.fa.gz 1:1000000-1000020

# Now the files are ready to use with fill-aa. Note that the VCF file
# should be sorted (see vcf-sort), otherwise the performance would be seriously
# affected.
cat file.vcf | fill-aa -a human_ancestor_ 2>test.err | gzip -c >out.vcf.gz

Hope this helps,

I am trying to run:
cat chr3.vcf | fill-aa -a | gzip -c >out.sort.ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.geno                                                                                      types.vcf

But I am getting the following error:

[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.
at /usr/local/share/perl5/ line 56.
FaSlice::throw('FaSlice=HASH(0x2227f08)', '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/ line 79
FaSlice::cmd('FaSlice=HASH(0x2227f08)', 'samtools faidx human_ancestor_3 \.fa\.bz 3\:60069\-160069') called at /usr/local/share/perl5/ line 125
FaSlice::read_chunk('FaSlice=HASH(0x2227f08)', 3, 60069) called at /usr/ local/share/perl5/ line 153
FaSlice::get_base('FaSlice=HASH(0x2227f08)', 3, 60069) called at /usr/lo cal/bin/fill-aa line 148
main::fill_aa('HASH(0x1d52a68)', '') called at /us r/local/bin/fill-aa line 18
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