lobstr-code
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mgymrek
lobSTR: a short tandem repeat profiler for next generation sequencing data
Hi, I did perform a test using the hg19_v3.0.2/tmp_1.fq/tmp_2.fq files provided in lobstr-code and it did generate test.aligned.bam, test.aligned.stats, test.vcf, and test.allelotype.stats. I have sequence-capture illumina data and I'm trying...
ERROR: command 'intersectBed -a /tmp/tmpeUwvrC/lobSTR_ref_merged.bed -b /tmp/tmpeUwvrC/lobSTR_ref_plusflank_sorted.bed -wa -wb | awk '{print $1 "\t" $2 "\t" $3 "\t" $7"_"$8"_"$9";"}' | bedtools groupby -g 1,2,3 -c 4 -o concat > index_dir/lobSTR_mergedref.bed'...
Your website is redirected to some porn site :) "For full documentation, see the lobSTR website: http://lobstr.teamerlich.org/"
Hello! I think this is a great tool. I was wondering if you know if it works to reconstruct STRs from ancient DNA whole genome sequencing. Thanks!
This is the version that i used 'allelotype-4.0.6'.The align software that i used is bwa-mem.So when i put in too many(3048 samples) of bam files ,it will report an error...
Dear Author, I have generated VCF file for lobSTR and use vcftools to get STR frequency (see below): CHROM POS N_ALLELES N_CHR {ALLELE:FREQ} chr14 16035037 3 130 TTTTCTTTTCTTTTCTTTTTTTTTTTTCTTTTCTTTCTTTTCTTTTCTTT:0.938462 TTTTCTTTTCTTTTCTTTTTTTTTTTTCTTTTCTTTCTTTTCTTTTCTTTT:0.0461538 TTTTCTTTTCTTTTCTTTTTTTTTTTTCTTTTCTTTCTTTTCTTTTCTTTTT:0.0153846...
We should build an hg38 reference and post to the website, and add scripts for the TRF step to the repo.
lobSTR seems to mis-genotype reads (or at least some reads) where the STR (in this case, a poly-G region) has an N in the middle. Is there any way to...
Hello, I am on of the contributor for homebrew and recently new version of g++5 and boost have been updated and there is error: ``` ==> brew install --build-bottle --verbose...
