I have been looking for an answer to my problem in all the Galaxy
Support resources but with no success. I am sorry if this topic has been
So, I am analyzing MiSeq data on the main Galaxy.
I have Fastq files from 4 paired-end samples. After having checked the
quality with FastQC and groomed them, I have performed a BWA mapping,
filtered the results and converted the SAM to BAM files (for each sample
separately). I have then called SNPs with Freebayes and SAMtools,
encountering problems in both cases.
1) SAMtools: if I run the Generate pileup tool, then the Filter pileup
doesn't recognize any valid format in the files I have in my History and
I cannot go on with the analysis. Why is that? What can I do?
2) I have performed variant calling with Freebayes on single BAM files
and on one merged BAM files from all my four BWA mapping files. In all
cases, the last column is "unknown", while it should be the name of my
sample. This is not a big deal for the single vcf files, but from the
merged BAM file, I cannot discriminate from which sample the SNPs were
detected. I think there is a problem in the BAM files which are not
properly indexed. Also Freebayes needs an RG tag.
Is there a tool in Galaxy I can use to index BAM files, adding the RG tag?
I hope someone can help me!
Thank you very much!
Debora Garzetti, PhD Student
Max von Pettenkofer-Institute, LMU
Phone: +49 (0)89 2180 72915
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