NM and nM tags are sanitized by replacement with 1.
MD are matched to the BAMboozled sequence, if present (eg.CIGAR value is matched to the BAMboozled sequence (eg.Unmapped reads: Unmapped reads cannot be sanitized and are discarded in default settings.ĭonor-related information could also be inferred from standard bam fields and auxiliary tags:.The user can choose to keep secondary but note that anonymization can not be guaranteed. Multimapping: In the default behavior, only primary alignments are emitted.Splicing: Splicing is observed and splice-sites are conserved even in the case of deletions and insertions.Instead for paired-end reads, the clipped sequence portion is added to the end of the read. If reads start with clipped bases in single-end data, the reference position of the read start is adjusted, however this is not possible for paired-end reads because it would invalidate the mate-pair information (TLEN and PNEXT fields). Clipping: soft or hard clipped bases (CIGAR: S / H) are replaced by matching reference sequence.Deletions: The missing reference sequence is inserted into the read while removing an equal numbers of bases from the 3’ end.Insertions: The read sequence is extended by the length equal to the insertion while keeping the 5' mapping position constant.SNPs: Mismatches to the reference (either explicitly X coded in the CIGAR value or within M matched segments) are replaced by the reference base.Here is an overview of the sequence correction strategy: The BAMboozle procedure involves modification of the observed read sequence to the reference genome sequence and sanitation of auxiliary tags. keepunmapped Keep ummapped reads in output bam file.īAMboozle sanitizes sequence reads to provide privacy protection and facilitate data sharing. keepsecondary Keep secondary alignments in output bam file. strict Strict: also sanitize mapping score & auxiliary tags (eg. fa FILENAME Path to genome reference fasta h, -help show this help message and exit bam file should be coordinate sorted and indexed, however BAMboozle.py will try to do this for you if not. Your fasta file should be indexed ( samtools faidx). bam file and the reference genome in fasta format. UsageīAMboozle.py requires only an aligned. To install, type the following command line, and add -U for upgrading:Īlternatively, you can install from this GitHub repository for the latest version:Īdd -user if you don't have write permissions in your default python folder. InstallationīAMboozle.py is available through PyPI. BAMboozle.py: de-identification of sequencing readsīAMboozle.py is a tool that can remove genetic variation from sequencing reads stored in BAM file format to protect the privacy and genetic information of donor individuals.
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