Pysam protocols

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Pysam specifications

Information


Unique identifier OMICS_19073
Name Pysam
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM,BAM,VCF,BCF,BED,GFF,GTF,FASTA,FASTQ
Output format SAM, BAM, VCF, BCF
Operating system Unix/Linux
Programming languages C, Python
License MIT License
Computer skills Advanced
Version 0.13
Stability Stable
Maintained Yes

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Additional information


https://readthedocs.org/projects/pysam/

Pysam in pipelines

 (9)
2018
PMCID: 5919577
PMID: 29698444
DOI: 10.1371/journal.pone.0196434

[…] score of ≥30, probability score of ≥0.90, and coverage ≥500., basic statistics of total reads, and reads mapped were generated using bespoke scripts in python including the packages biopython and pysam and plots drawn using matplotlib. to compare read counts between three discrete groups the kruskal-wallis test was performed, and comparison over time was performed using linear regression, […]

2017
PMCID: 5553663
PMID: 28800727
DOI: 10.1186/s12864-017-4013-y

[…] using the michigan imputation server [], the 1000 genomes phase 3 v5 reference panel, and the eagle phasing algorithm to obtain phased output [, ]. we developed a python script based on vcf and pysam python modules to read snp information and assign the haplotype accordingly [, ]. code and an example are available on github (https://github.com/eshaikho/haplotypeclassifier). we used […]

2016
PMCID: 4948782
PMID: 27428049
DOI: 10.1371/journal.pgen.1006162

[…] human genome using bwa mem (v. 0.7.9a-r786) and insert size metrics for each sample were assessed using picard tools (v. 1.107). tumor fraction as a function of insert size was analyzed using the pysam samtools api., libraries for illumina high throughput sequencing were prepared using the kapa biosystems hyper prep kit with 10 ng input cell-free dna according to the manufacturer’s […]

2016
PMCID: 5070307
PMID: 27756224
DOI: 10.1186/s12864-016-3154-8

[…] stage reads were aligned for each clone. alignment files were manipulated using samtools [], and visualized in the artemis genome browser []. single base resolution plots were generated using the pysam api (https://github.com/pysam-developers/pysam) in an in-house script that filters reads based on alignment quality (mapq) and corrects for library size (available on request). trans-spliced […]

2016
PMCID: 5082946
PMID: 27788196
DOI: 10.1371/journal.pone.0165375

[…] p-hm2 genomes using the burrows–wheeler aligner (bwa). genbank annotations (bx548174.1 for med4 and nc_015284.1 for p-hm2) were used to generate sam alignment files using bwa. samtools [] and pysam were then used to calculate the number of reads perfectly aligning to the sense and antisense strands of orfs, rrnas, trnas, and intergenic regions. paired reads were mapped separately; paired […]


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Pysam in publications

 (45)
PMCID: 5919577
PMID: 29698444
DOI: 10.1371/journal.pone.0196434

[…] score of ≥30, probability score of ≥0.90, and coverage ≥500., basic statistics of total reads, and reads mapped were generated using bespoke scripts in python including the packages biopython and pysam and plots drawn using matplotlib. to compare read counts between three discrete groups the kruskal-wallis test was performed, and comparison over time was performed using linear regression, […]

PMCID: 5855702
PMID: 29415469
DOI: 10.3390/ijms19020480

[…] encff913mgs, encff374xwq, and encff833pxb) were downloaded from http://www.encodeproject.org and indexed with samtools. read densities were visualized using the igv browser and analyzed using the pysam module in python., tcga gbm rna-seq data were retrieved from cancer rna-seq nexus database (http://syslab4.nchu.edu.tw/)., genes, mrnas and proteins are named according to the guidelines set […]

PMCID: 5759210
PMID: 29310578
DOI: 10.1186/s12864-017-4409-8

[…] to the 32 variant reference sequences using bowtie2/tophat2 [, ]. the counts of read-sequences mapped to each variant, and the properties of each alignment, were retrieved using scripts based on pysam module (http://code.google.com/p/pysam/). another method of mapping that counted and estimated proportions of a/g/t/c nucleotides (nucleotide pileup) at each edited site separately was used. […]

PMCID: 5647807
PMID: 28985307
DOI: 10.1093/gbe/evx190

[…] er.sourceforge.net/) for job scheduling. read mapping qualities <30 were discarded and only the top highest mapq scored reads in the case of duplicates were retained. pileups were created with the pysam (available at http://code.google.com/p/pysam) interface to samtools () and sites with base quality scores <25 were discarded. valid alleles were represented on >8 reads and a frequency > […]

PMCID: 5635981
PMID: 28847005
DOI: 10.1038/nature23670

[…] a sequence length comprises between 50 bp and 2000 bp. genome coverage was processed by bedtools (http://bedtools.readthedocs.io/en/latest/index.html, v2.26.0) and a dedicated python script using pysam (https://github.com/pysam-developers/pysam) was written to identify potential insert. briefly, in both workflows (2 and 40 reads), potential inserts were assigned if they fulfilled […]


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