A junk drawer of one-off scripts that don't deserve their own repo yet.
Identify low-complexity sequence in a fasta file and output a bed file with annotated homopolymers and dinucleotide repeats.
usage: repeat_bed.py [-h] [--minhrun MINHRUN] [--minrepeats MINREPEATS]
[--threads {1,2,3,4,5,6,7}]
reference
Identify low-complexity regions in a fasta file. Outputs a bed file with
annotated homopolymers and dinucleotide streches.
positional arguments:
reference path for input fasta
optional arguments:
-h, --help show this help message and exit
--minhrun MINHRUN minimum homopolymer run length (0=disabled)
--minrepeats MINREPEATS
minimum dinucleotide repeats (0=disabled)
--threads {1,2,3,4,5,6,7}
number of threads (1)
Add tag mq to reads in BAM, with a binned representation of the MAPQ (MAPQ/10).
usage: samtools view my.bam | python3 add_mq_tag.py > my.mq.bam
Add FORMAT field for variant allele fraction to pbsv VCF.
usage: cat pbsv.vcf | python3 add_vaf.py > pbsv.vaf.vcf
For a mosdepth bed file provided to stdin, determine the mean and stddev as if the data were normally distributed, and report these values.
usage: tabix ${BAM%.*}.median.regions.bed.gz <list of autosomes> | python depth_mean_stddev.py
usage: extract_aligned_fasta.py [-h] inbam outfasta contig start stop
Extract subsequences mapped to contig:start-stop.
Given an aligned bam and coordinates, return the reference-oriented
subsequences of alignments that completely overlap [start, stop].
positional arguments:
inbam input bam
outfasta output fasta
contig reference contig
start start position on reference contig
stop stop position on reference contig
optional arguments:
-h, --help show this help message and exit
usage: extract_aligned_fastq.py [-h] inbam outfastq contig start stop
Extract subsequences mapped to contig:start-stop.
Given an aligned bam and coordinates, return the subsequences of alignments
that completely overlap [start, stop].
positional arguments:
inbam input bam
outfastq output fastq
contig reference contig
start start position on reference contig
stop stop position on reference contig
optional arguments:
-h, --help show this help message and exit
usage: gen_fp_fn_tracks.py [-h] invcf
Split hap.py annotated vcf into variant types and false call types.
positional arguments:
invcf hap.py vcf with annotated FP and FN
optional arguments:
-h, --help show this help message and exit
Mark duplicate reads in input BAM and write to output BAM. Reference based.
usage:
python markdup_stream.py --inbam consensusalignments.bam \
--outbam markdup.consensusalignments.bam \
--stats dedup.stats.txt \
--dup_list dupreads.txt
Mark duplicate reads in input BAM and write to output BAM
usage:
python markdup_stream.py --inbam consensusalignments.bam \
--outbam markdup.consensusalignments.bam \
--stats dedup.stats.txt \
--dup_list dupreads.txt
Calculate alignment of sequences flanking adaptor and plot distribution. CCS reads from SMRTbell templates missing one adaptor should result in palindromic reads. This script attempts to identify these reads by aligning bases that flank the adaptor. The outputs are a histogram of normalized alignment score (so you can pick a threshold that fits your data) and a table with alignment scores and other useful per-read stats, so that you can easily create whitelists. My early attempts at aligning the full CCS read to its reverse complement 1) resulted in distributions that were difficult to explain and 2) took too long for large datasets. Comparing the first and last N bases in the CCS read solved both of those problems. The tradeoff is that this method might be less robust to biological repeats. One can always change the number of flanking bases used if desired. The constants at the top are empirically chosen for bimodal separation after testing on a couple datasets. YMMV.
usage: missing_adaptor.py [-h] [--nohist] fasta
Given a vcf, create a bed of intervals between consecutive heterozygous variants.
usage: vcfhet2bed.py [-h] vcf chromosome
Convert 1KGP VCF to BED of het var intervals
positional arguments:
vcf 1KGP vcf
chromosome chromosome
optional arguments:
-h, --help show this help message and exit
Helper functions for compressing homopolymers and calculating a DNA zCurve.