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<prev • 105 results • page 1 of 4 • next >
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How to calculate VAF from BAM or SAM(+pileups) files using pysam?
bam vaf pysam snp sequencing written 27 days ago by askif4 • 0
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124
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0
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Check for deletions at particular neighboring positions - Pysam pileup or fetch
deletions deleted bases pysam pileup fetch written 7 weeks ago by z.klinovska • 0
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1
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115
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1
answer
How to determine mutation type/subtype via pysam/samtools
vcf type samtools pysam snp written 10 weeks ago by mike.rightmire • 0 • updated 10 weeks ago by Pierre Lindenbaum ♦ 133k
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384
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How to get inserted bases using pysam pileup
next-gen alignment pysam bam written 8 months ago by va90 • 10 • updated 3 months ago by Lhl • 730
1
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1
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137
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1
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pysam doesn't calculate correct nucleotide quantities from .bam file
count pysam python written 3 months ago by vit.filippo • 50 • updated 3 months ago by dariober ♦ 11k
3
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3
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2.3k
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3
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Get all the nucleotides from a bam file that is aligning to specific position in the genome
genome samtools alignment position pysam written 2.5 years ago by rsafavi • 50 • updated 4 months ago by Kevin Blighe ♦ 69k
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247
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Pysam, how to calculate how many bases on the reference are covered by reads?
bam samtools pysam written 5 months ago by Dgg32 • 90
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1
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219
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1
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Error on pysam.bcftools.mpileup: "Segmentation fault (core dumped)"
bcftools samtools pysam mpileup written 5 months ago by sbstevenlee • 0
6
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2
answers
220
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2
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Incorrect sequence retrieved by coordinates
fasta python biopython pysam written 6 months ago by Igor Filippov • 0 • updated 6 months ago by Istvan Albert ♦♦ 86k
3
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2
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293
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2
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How to add "OQ" tag with read quality score as additional field in the bam file using pysam
wgs bam pysam bqsr readquality written 6 months ago by gnanakkan • 0
0
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1
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242
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1
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Pysam pileup method gives more columns than expected
python pysam written 7 months ago by Didrik.Olofsson • 0 • updated 7 months ago by khorms • 210
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215
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How to add a flag to the INFO column of a vcf with pysam?
vcf bcf pysam written 7 months ago by curious • 470
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189
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pysam pileup doesn't work when contig name is specified?
pysam pileup coverage depth written 7 months ago by dp • 40
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176
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read and write a bam: but duplicate the quality column (11) and write one with "OQ:Z:" flag
alignment samtools base quality bam pysam written 9 months ago by gnanakkan • 0 • updated 7 months ago by Biostar ♦♦ 20
0
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0
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208
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Type error in argument header
alignment pysam written 8 months ago by sam • 0
8
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2
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5.3k
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7 follow
2
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How to filter/view reads mapped to multiple locations using samtools or pysam
python samtools pysam written 3.9 years ago by AlchemistMoz • 20 • updated 9 months ago by jaeyoung.chun • 30
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Error during htseq-count
htseq-count star pysam written 3.4 years ago by baffiak1902 • 10 • updated 10 months ago by Biostar ♦♦ 20
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407
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Pysam get query sequence range without loop
python pysam written 11 months ago by yryan • 0
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0
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435
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Pysam pileup dropping reads
pysam pileup written 11 months ago by yryan • 0
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1
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445
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1
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understanding pysam.AlignmentFile output
bam pysam sam written 12 months ago by bitpir • 190 • updated 12 months ago by onestop_data • 250
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1
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817
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1
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Difference between Pysam Pileup and Fetch
reads bam pysam pileup written 16 months ago by aalith • 10 • updated 13 months ago by castaway1990 • 0
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302
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Trim each read from bam file
trimbam bam pysam written 13 months ago by SSK • 10
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1.2k
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0
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Import Module error Pysam
pysam snp written 16 months ago by prahalad.atreyaa • 0 • updated 14 months ago by Biostar ♦♦ 20
1
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2
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600
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2
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suppress pysam index warnings.
python bam pysam written 14 months ago by b10hazard • 30 • updated 14 months ago by John Marshall ♦ 2.2k
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1
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254
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1
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Mapping quality score of clipped reads
python bam pysam written 14 months ago by radwa.raed • 10 • updated 14 months ago by swbarnes2 ♦ 9.3k
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1
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358
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5 follow
1
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Pipe pysam.view() output to pysam.sort()
python sam alignment pysam sort written 15 months ago by Macspider • 3.3k • updated 15 months ago by gb • 1.9k
0
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1
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541
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1
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Pysam not finding mapped reads in BAM file
chip-seq bam samtools pysam written 17 months ago by taraeicher • 30
1
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1
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737
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1
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Parsing tabix with pysam
tabix pysam written 18 months ago by Alex Reynolds ♦ 31k • updated 18 months ago by John Marshall ♦ 2.2k
2
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1
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581
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1
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Finding all bases at a specific genomic position
pysam pileup written 18 months ago by dodani • 0
2
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1
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1.7k
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1
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Error Filtering BAM file based on mapping qualities in python's pysam
next-gen alignment pysam written 4.1 years ago by ammarsabir15 • 60 • updated 19 months ago by Biostar ♦♦ 20
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