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- Andrea Guarracino
Hi @bhanuGandham, for data preprocessing I I took inspiration (and the instructions) from the five-dollar-genome -analysis pipeline. From (bbduk-)adapter-trimmed FASTQ files converted in an unmapped BAM file, I follow the following steps: * SamToFa…
Hi @bhanuGandham and @micknudsen, thanks for your support. Actually, I am following the Best Practices with the only difference in the adapter trimming step where I use BBduk: with the trimmed FASTQ files I create the uBAM file to use as input for …
@Tiffany_at_Broad, I wrote the post for the other users, I don't have any question about it, thank you!
(Quote) Hi @Sheila, maybe meanwhile something changed somewhere in the documentation, but at the moment in the 1000G_phase1.snps.high_confidence.hg38.vcf file there aren't indels (checked with vcftools keeping only indels).
@AdelaideR I am sorry for the late answer. Yes, the file I received were from different references. Thank you all.
Thank you. I've created the dictionary and I've tried this command: java -jar tools/picard.jar SortVcf I=data/mongolian/Mongolian_genome_sorted_noChr2.snp.vcf O=data/mongolian/Mongolian_genome_sorted_noChr2_SortVcf.vcf SEQUENCE_DICTIONARY=data/hum…