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  • 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 . --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 --allow_potentially_misencoded_quality_scores --emitRefConfidence GVCF -variant_index_type LINEAR -variant_index_parameter 128000

    then i used GenotypeGVCFs to combine samples
    java -jar GenomeAnalysisTK.jar \
    -T GenotypeGVCFs \
    -R pe.scaffolds.db.fasta \
    --variant 123480.raw_variants.g.vcf \
    --variant 123651.raw_variants.g.vcf \
    -o 56species_raw.vcf \

    and, i used SelectVariants like this:
    java -jar GenomeAnalysisTK.jar \
    -T SelectVariants \
    -R pe.scaffolds.db.fasta \
    -V 56species_raw.vcf \
    -L PH01000000 \
    -ef \
    -o 56species_test.vcf

    i get the vcf files, then i used vcftools convert the vcf file to fasta file. but i found that in the fasta file, different samples have different number of loci. i want to do phylogenetic analysis, now, i do not know how to solve the problem.

  • #2
    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?

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