Hi, I’m a beginner on Galaxy and I’m trying to use ANNOVAR on VCF files from exome (it’s all I have). Variant caller used was Samtool. VCF files have been mapped on hg19, and I filled this information when I imported my data. But each time I used ANNOVAR after filter out on severals genes (on hg19) and DP, either exporting on VCF format, either on tabular, I obtain a 0 line files despite I haven’t had error message, I have this:
NOTICE: Finished reading 389 lines from VCF file
NOTICE: A total of 356 locus in VCF file passed QC threshold, representing 317 SNPs (225 transitions and 92 transversions) and 42 indels/substitutions
NOTICE: Finished writting 317 SNPs (225 transitions an
Then the message is cut.
Is it a question of conversion between Samtool or anything else ?
Thank you a lot for any information