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I used Galaxy to generate vcf files, but the output has unphased genotypes. Are there any options for obtaining the phased genotypes through Galaxy?
My data were generated from 350 bp amplicons sequenced on the Ion Torrent PGM platform (400 bp sequencing kit). I used BarcodeSplitter on my FASTQ files, uploaded my own reference sequence, then followed these steps:
1) Filter FastQ (minimum 350 bp)
2) FastQ Trimmer (remove 10 bp barcodes)
3) Map with BWA (Illumina setting)
4) SAM-to-BAM
5) MPileup
6) Pileup-to-VCF
I also tried using GATK Unified Genotyper and FreeBayes on my output from BWA. Any suggestions appreciated.
My data were generated from 350 bp amplicons sequenced on the Ion Torrent PGM platform (400 bp sequencing kit). I used BarcodeSplitter on my FASTQ files, uploaded my own reference sequence, then followed these steps:
1) Filter FastQ (minimum 350 bp)
2) FastQ Trimmer (remove 10 bp barcodes)
3) Map with BWA (Illumina setting)
4) SAM-to-BAM
5) MPileup
6) Pileup-to-VCF
I also tried using GATK Unified Genotyper and FreeBayes on my output from BWA. Any suggestions appreciated.