Showing: samtoolsreset
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2
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Genotyping with samtools/bcftools
samtools ngs bcftools written 3 days ago by SOHAIL200 • updated 3 days ago by Kevin Blighe24k
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111
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1
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19
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9 follow
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Extracting Paired-End Reads Sitting In Different Chromosomes
paired samtools written 6.4 years ago by Ian5.2k • updated 3 days ago by Stephane Plaisance360
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132
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6 follow
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Merge .bam files by groups of lanes
bam samtools rna-seq written 4 days ago by elb110 • updated 4 days ago by WouterDeCoster30k
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Extract the SAM File header section
htsjdk java bam samtools sam written 5 days ago by mhasa00630 • updated 4 days ago by Pierre Lindenbaum110k
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103
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1
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VCF files-Keep all alternative alleles
vcf bcftools samtools vcftools snp written 5 days ago by juara10 • updated 5 days ago by Pierre Lindenbaum110k
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139
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5 follow
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11
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Can´T Find The Snps With Samtools (Only Get Indels)
indel alignment samtools snp written 6.9 years ago by Pilar E.90 • updated 6 days ago by Biostar ♦♦ 20
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115
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7 follow
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Samtools mpileup degenerative characters
samtools degenrative characters mpileup written 12 months ago by divya20 • updated 10 days ago by swbarnes23.8k
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106
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3
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Extract R1 and R2 bam files from merged bam file
samtools rna-seq written 11 days ago by chahat_u50 • updated 11 days ago by h.mon16k
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5
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Format in vcf files in Geuvadis data not recognized
vcf samtools format bcftools geuvadis written 12 days ago by jamespower20 • updated 12 days ago by Pierre Lindenbaum110k
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133
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Why does this samtools command work?
samtools rna-seq written 12 days ago by chahat_u50 • updated 12 days ago by h.mon16k
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Size different between two uBam file which generate from the same Fastq.
gatk bam samtools written 12 days ago by weichi10 • updated 12 days ago by h.mon16k
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8 follow
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No alignment, only header in sam file
samtools unix rna-seq written 13 days ago by ss0 • updated 12 days ago by ATpoint5.7k
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144
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3
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How To Filter Against Common Snp Database To Look For Rare Variants?
samtools snp written 6.3 years ago by Bioscientist1.6k • updated 16 days ago by Biostar ♦♦ 20
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GBS SNPs calling
fast-gbs gatk snp calling samtools gbs written 17 months ago by shinken12350 • updated 18 days ago by Arthur Melo0
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Adding tag XS to HISAT2 sam files perior to StringTie
stringtie alignment samtools rna-seq hisat2 written 22 days ago by Farbod3.1k • updated 22 days ago by Vijay Lakhujani2.8k
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149
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5 follow
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Can you get mpileup to report positions with coverage of 0?
samtools mpileup written 23 days ago by blur90 • updated 23 days ago by Devon Ryan81k
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Sorting samtools output by flag or grepping its tags
flag grep samtools chimeric written 11 months ago by BPors30 • updated 25 days ago by Biostar ♦♦ 20
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103
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Does samtools depth know how to handle paired-end reads
samtools coverage written 25 days ago by roy.granit700 • updated 25 days ago by ATpoint5.7k
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difference between mapq=0 and samtools flag 0x900
samtools mapq written 26 days ago by bitpir70 • updated 25 days ago by Devon Ryan81k
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132
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5 follow
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Filter sam/bam files
filter bam samtools sam gbs written 26 days ago by ramesh.8v200 • updated 26 days ago by swbarnes23.8k
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