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Pysam specifications


Unique identifier OMICS_19073
Name Pysam
Software type Package/Module
Interface Command line interface
Restrictions to use None
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




No version available


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Pysam citations


Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice

PLoS One
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, […]


CircSMARCA5 Inhibits Migration of Glioblastoma Multiforme Cells by Regulating a Molecular Axis Involving Splicing Factors SRSF1/SRSF3/PTB

Int J Mol Sci
PMCID: 5855702
PMID: 29415469
DOI: 10.3390/ijms19020480

[…] encff913mgs, encff374xwq, and encff833pxb) were downloaded from 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 (, genes, mrnas and proteins are named according to the guidelines set […]


A to I RNA editing in the rat brain is age dependent, region specific and sensitive to environmental stress across generations

BMC Genomics
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 ( another method of mapping that counted and estimated proportions of a/g/t/c nucleotides (nucleotide pileup) at each edited site separately was used. […]


Sequence Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis)

Genome Biol Evol
PMCID: 5647807
PMID: 28985307
DOI: 10.1093/gbe/evx190

[…] 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 interface to samtools () and sites with base quality scores <25 were discarded. valid alleles were represented on >8 reads and a frequency > […]


Public antibodies to malaria antigens generated by two LAIR1 insertion modalities

PMCID: 5635981
PMID: 28847005
DOI: 10.1038/nature23670

[…] a sequence length comprises between 50 bp and 2000 bp. genome coverage was processed by bedtools (, v2.26.0) and a dedicated python script using pysam ( was written to identify potential insert. briefly, in both workflows (2 and 40 reads), potential inserts were assigned if they fulfilled […]


Facile single stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switching

Sci Rep
PMCID: 5566474
PMID: 28827600
DOI: 10.1038/s41598-017-09064-w

[…] v2.5 (broad institute). gini coefficients are computed by ineq package from r., base substitution rates, indel rates, and nucleotide composition biases were extracted by customized scripts using pysam package. simulated datasets for the e. coli k12 genome were created with customized scripts using pyfaidx and scipy packages following a previously described algorithm,,. all plots were done […]

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