annovar with worm data
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Entering edit mode
8 months ago
scheitelt ▴ 10

Hi,

has anybody worked with annovar in the past with worm (Saccharomyces cerevisiae)? I'm trying to annotate my vcf files but keep getting into trouble, first downloading any kind of data base, then downloading sequences.

I think this is one of the worst documented tools ever.

Can anyone tell me, what am I doing wrong here

# download the gene information
annotate_variation.pl -buildver sacCer3 -downdb -webfrom  ucsc sgdGene Scedb/

# annotating the vcf file
table_annovar.pl jointSamples.vcf Scedb/ -buildver scaCer3 -out jointSamples_annovar.vcf -remove -protocol sgdGene -operation g -nastring . -vcfinput -polish

But with this I get the following error

NOTICE: Running with system command <convert2annovar.pl -includeinfo="" -allsample="" -withfreq="" -format="" vcf4="" ..="" gallegos="" samtools="" results.bcftools="" jointsamples.vcf="" &gt;="" jointsamples_annovar.vcf.avinput=""> NOTICE: Finished reading 364 lines from VCF file NOTICE: A total of 319 locus in VCF file passed QC threshold, representing 228 SNPs (125 transitions and 103 transversions) and 91 indels/substitutions NOTICE: Finished writing allele frequencies based on 1824 SNP genotypes (1000 transitions and 824 transversions) and 728 indels/substitutions for 8 samples

NOTICE: Running with system command </home>

NOTICE: Processing operation=g protocol=sgdGene

NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver sacCer3 -dbtype sgdGene -outfile jointSamples_annovar.vcf.sgdGene -exonsort -nofirstcodondel jointSamples_annovar.vcf.avinput Scedb/>
NOTICE: Output files are written to jointSamples_annovar.vcf.sgdGene.variant_function, jointSamples_annovar.vcf.sgdGene.exonic_variant_function
NOTICE: Reading gene annotation from Scedb/sacCer3_sgdGene.txt ... Done with 6692 transcripts (including 0 without coding sequence annotation) for 6692 unique genes
NOTICE: Processing next batch with 319 unique variants in 319 input lines
Error: FASTA sequence file Scedb/sacCer3_sgdGeneMrna.fa does not exist. Please use 'annotate_variation.pl --downdb sgdGene Scedb' download the database.
Error running system command: <annotate_variation.pl -geneanno -buildver sacCer3 -dbtype sgdGene -outfile jointSamples_annovar.vcf.sgdGene -exonsort -nofirstcodondel jointSamples_annovar.vcf.avinput Scedb/>
Error running system command: <software/annovar/table_annovar.pl jointSamples_annovar.vcf.avinput Scedb/ -buildver sacCer3 -outfile jointSamples_annovar.vcf -remove -protocol sgdGene -operation g -nastring . -polish -otherinfo>

But when I try to download any kind of sequences, they are not on the ucsc server.

Does anyone has good alternatives for annovar ( or any alternative, as almost anythin is better than this tool )?

thanks

annovar sacCer3 worm variant_detection • 210 views
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Entering edit mode

isn't it your error ?

Error: FASTA sequence file Scedb/sacCer3_sgdGeneMrna.fa does not exist.

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Entering edit mode

thanks Pierre,

yes this is the (an?) error, but the suggested solution doesn't work. I have tried several different solutions, but couldn't make it run.

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