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Forum: Bioinformatics 09-04-2015, 10:36 PM
Replies: 1
Views: 1,388
Posted By wangxueqin
i used bowtie+samtools also, i converted the vcf...

i used bowtie+samtools also, i converted the vcf file to fasta file. in the fasta file, evry samples had the same length. so i wonder may be i set the wrong parameters in GATK?
Forum: Bioinformatics 09-04-2015, 09:45 PM
Replies: 1
Views: 1,388
Posted By wangxueqin
vcf convert to fasta, the fasta file is not an alingment file

i have multiple samples. i used HaplotypeCaller in GATK like:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R ./pe.scaffolds.db.fasta -I ./AEM.dedupped.bam -o ./AEM.raw_variants.g.vcf ....
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