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Comment: Comment: Best way to deal with overlapping read names in merged BAM files
25 days ago by shpak.max ▴ 50
0
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1
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437
views
Comment: Comment: Best way to deal with overlapping read names in merged BAM files
25 days ago by shpak.max ▴ 50
1
vote
5
replies
437
views
Best way to deal with overlapping read names in merged BAM files
picard MarkDuplicates
25 days ago by shpak.max ▴ 50
0
votes
1
reply
286
views
Comment: Comment: Multiple iterations of sorted bam output files with picard SortSam
5 weeks ago by shpak.max ▴ 50
0
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3
replies
286
views
Multiple iterations of sorted bam output files with picard SortSam
picard
updated 5 weeks ago by 142k • written 5 weeks ago by ▴ 50
0
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0
replies
494
views
Comment: Comment: java version compatible with GATK 3.2.2
8 weeks ago by shpak.max ▴ 50
0
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1
reply
494
views
Comment: Comment: java version compatible with GATK 3.2.2
8 weeks ago by shpak.max ▴ 50
0
votes
0
replies
494
views
Comment: Comment: java version compatible with GATK 3.2.2
8 weeks ago by shpak.max ▴ 50
0
votes
0
replies
494
views
Comment: Comment: java version compatible with GATK 3.2.2
8 weeks ago by shpak.max ▴ 50
1
vote
7
replies
494
views
java version compatible with GATK 3.2.2
GATK
8 weeks ago by shpak.max ▴ 50
0
votes
1
reply
311
views
Comment: Comment: Merging bam files from different runs
8 weeks ago by shpak.max ▴ 50
0
votes
1
reply
311
views
Comment: Comment: Merging bam files from different runs
8 weeks ago by shpak.max ▴ 50
1
vote
5
replies
311
views
Merging bam files from different runs
samtools bam
updated 8 weeks ago by 142k • written 8 weeks ago by ▴ 50
0
votes
5
replies
1.1k
views
Stampy make fails
Stampy
updated 3 months ago by • 0 • written 2.8 years ago by ▴ 50
0
votes
0
replies
801
views
Comment: Comment: Detecting heterozygous deletions in NGS sequence data
13 months ago by shpak.max ▴ 50
1
vote
3
replies
801
views
Detecting heterozygous deletions in NGS sequence data
fastq vcf GATK
13 months ago by shpak.max ▴ 50
0
votes
1
reply
698
views
Comment: Comment: Read lengths greater than insert length
13 months ago by shpak.max ▴ 50
5
votes
3
replies
698
views
Read lengths greater than insert length
NGS
updated 13 months ago by 142k • written 13 months ago by ▴ 50
0
votes
1
reply
831
views
Comment: Comment: Identifying adapter sequence to trim for Illumina IIx data
20 months ago by shpak.max ▴ 50
0
votes
3
replies
831
views
Identifying adapter sequence to trim for Illumina IIx data
trimmomatic
updated 20 months ago by 14k • written 20 months ago by ▴ 50
0
votes
0
replies
1.2k
views
Comment: Comment: How does one use rename in seqkit to change sequence labels
20 months ago by shpak.max ▴ 50
2
votes
3
replies
1.2k
views
How does one use rename in seqkit to change sequence labels
seqkit
20 months ago by shpak.max ▴ 50
0
votes
1
reply
1.6k
views
Comment: Comment: Treating forward and reverse reads independently in BWA
20 months ago by shpak.max ▴ 50
0
votes
1
reply
1.6k
views
Comment: Comment: Treating forward and reverse reads independently in BWA
20 months ago by shpak.max ▴ 50
0
votes
0
replies
1.6k
views
Comment: Comment: Treating forward and reverse reads independently in BWA
20 months ago by shpak.max ▴ 50
0
votes
2
replies
1.6k
views
Comment: Comment: Treating forward and reverse reads independently in BWA
20 months ago by shpak.max ▴ 50
1
vote
10
replies
1.6k
views
Treating forward and reverse reads independently in BWA
bwa
updated 20 months ago by 100k • written 20 months ago by ▴ 50
0
votes
0
replies
680
views
Comment: Comment: Sampling short reads from a library with long reads
20 months ago by shpak.max ▴ 50
0
votes
2
replies
680
views
Sampling short reads from a library with long reads
alignments bwa
20 months ago by shpak.max ▴ 50
0
votes
0
replies
1.4k
views
Comment: Comment: fastq-dump throws "connection failed" error
23 months ago by shpak.max ▴ 50
0
votes
2
replies
1.4k
views
fastq-dump throws "connection failed" error
SRA fastq fastq-dump
23 months ago by shpak.max ▴ 50
1
vote
0
replies
343
views
Identifying/filtering pairwise IBD regions in diploid genomes
IBD
2.2 years ago by shpak.max ▴ 50
0
votes
0
replies
2.3k
views
Comment: Comment: Using IndexFeatureFile to index vcf
2.4 years ago by shpak.max ▴ 50
2
votes
2
replies
2.3k
views
Using IndexFeatureFile to index vcf
GATK
2.4 years ago by shpak.max ▴ 50
0
votes
0
replies
931
views
Comment: Comment: Comparing SNP coordinates from alignments to different reference genomes
2.5 years ago by shpak.max ▴ 50
0
votes
2
replies
931
views
Comparing SNP coordinates from alignments to different reference genomes
Samtools
2.5 years ago by shpak.max ▴ 50
0
votes
0
replies
1.6k
views
Comment: Comment: SAM Validation Error with CleanSam (Aligment start must be <= reference seq len
2.6 years ago by shpak.max ▴ 50
0
votes
1
reply
1.6k
views
Comment: Comment: SAM Validation Error with CleanSam (Aligment start must be <= reference seq len
2.6 years ago by shpak.max ▴ 50
0
votes
2
replies
1.6k
views
Comment: Comment: SAM Validation Error with CleanSam (Aligment start must be <= reference seq len
2.6 years ago by shpak.max ▴ 50
1
vote
7
replies
1.6k
views
SAM Validation Error with CleanSam (Aligment start must be <= reference seq length)
Samtools Picard
2.6 years ago by shpak.max ▴ 50
0
votes
0
replies
426
views
Using PoolSNP to return non-SNP genotypes
PoolSNP
2.6 years ago by shpak.max ▴ 50
0
votes
0
replies
445
views
Using UnifiedGenotyper on single chromosome without coordinates
GATK
2.7 years ago by shpak.max ▴ 50
0
votes
1
reply
1.2k
views
Comment: Comment: Genotyping low read depth sequences using GATK
2.7 years ago by shpak.max ▴ 50
0
votes
3
replies
1.2k
views
Genotyping low read depth sequences using GATK
GATK
updated 2.7 years ago by ★ 1.2k • written 2.7 years ago by ▴ 50
0
votes
0
replies
6.4k
views
Comment: Comment: bcftools consensus still returns "Could not parse the header" error
2.8 years ago by shpak.max ▴ 50
0
votes
2
replies
6.4k
views
Comment: Comment: bcftools consensus still returns "Could not parse the header" error
2.8 years ago by shpak.max ▴ 50
0
votes
5
replies
6.4k
views
bcftools consensus still returns "Could not parse the header" error
bcftools samtools
2.8 years ago by shpak.max ▴ 50
0
votes
1
reply
4.0k
views
Comment: Comment: Probable bug in bcftools while parsing headers
2.8 years ago by shpak.max ▴ 50
0
votes
0
replies
384
views
PoolSNP RuntimeError: dictionary changed size during iteration
Poolsnp
2.8 years ago by shpak.max ▴ 50
0
votes
1
reply
1.5k
views
bamdst gives error "EOF marker is absent. The input is probably truncated."
bwa samtools bamdst
updated 2.7 years ago by ▴ 270 • written 2.8 years ago by ▴ 50
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