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Thanks for your reply! So, I looked for headers as you said but I think I misunderstand something. That file, bams.list, is listing (indeed) all my sample like this: REALIGN/001.bam REALIGN/003.bam REALIGN/004.bam ... In replacement of all these -…
(Quote) RAD seq data, Ion Torrent sequencing. What I did is: * 8 Fastq files obtained (quality filtered) * Contaminants removed with Seqtrimnext * Fastq to fasta * Pseudo-ref created with CLC (from these 8 fasta files) * BWA alignment to pseudo ref…
(Quote) java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R pseudoref.fa -I [...] -glm BOTH -o res.vcf -drf DuplicateRead --filter_mismatching_base_and_quals -et NO_ET -K file.key (Quote) Any tips to get through this % problem?