Lobstr-code

lobSTR: a short tandem repeat profiler for next generation sequencing data

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Recommendations for setting lobSTR alignment parameters

Overview

General usage for running the lobSTR alignment step can be found on the usage and best practices for WGS/WES pages. This page gives advice on more specific topics related to alignment.

Read length recommendations

Depending on the length and type of your input reads, certain specific parameters might improve lobSTR performance.

Short reads

If aligning to the standard hg19 reference provided in the resource bundle, we recommend at least 100bp reads for the best quality alignments. However, read lengths as low as 50-70bp can give good results if you are primarily interested in STRs with a total length of ~20bp or less. Be aware that short reads will give very biased results for longer STRs: only short alleles that can be spanned by the read length will be detected, leading to a large bias toward reporting the shorter allele at heterozygous loci.

Long reads

lobSTR can also be used to align longer reads (several hundreds of bp). For very long reads, these parameters can be useful: Note that lobSTR aligns each read to a primary STR. If a read spans more than one STR, this will be noted in a flag ("XO"). However the allelotype step will only look at the primary STR aligned to (see specific applications below for how to bias lobSTR toward choosing certain types of STRs as the primary STR). We plan to change this in the future.

Specific applications

Based on the characteristics of the STRs you're interested in genotyping, it might be helpful to set some special flags:

Alignment sensitivity and specificity

lobSTR offers the following parameters to control alignment specificity and sensitivity:

Filtering output reads

You can use the following to filter which reads are output:

Multi-mappers

By default, lobSTR does not report alignments for reads that did map to a unique best location. To report these reads, use --multi. This will report one primary alignment and list alternative locations in the "XA" tag of the BAM file.

Speeding up alignment

To speed up lobSTR alignment, try: