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0
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0
replies
238
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Handling FILTER Fields in VCF Metadata and Body
VCF
12 weeks ago by ManuelDB ▴ 110
0
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0
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314
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Comment: Comment: Hard filtering to reduce false positive variants due to poly track sequences
3 months ago by ManuelDB ▴ 110
2
votes
2
replies
314
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Hard filtering to reduce false positive variants due to poly track sequences
GATK
updated 3 months ago by 147k • written 3 months ago by ▴ 110
0
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1
reply
289
views
Filtering Non-Homozygous and Non-Heterozygous Variants in DNA Analysis Pipeline
NGS
updated 3 months ago by 44k • written 3 months ago by ▴ 110
1
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0
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348
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Comment: Comment: Optimising False Positive Detection in NGS Pipelines Using Mapping and Base Qual
3 months ago by ManuelDB ▴ 110
2
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2
replies
348
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Optimising False Positive Detection in NGS Pipelines Using Mapping and Base Quality Scores
BaseQualityRankSumTest
3 months ago by ManuelDB ▴ 110
0
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0
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399
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Comment: Comment: Replace SB flag by PASS in my VCF file
4 months ago by ManuelDB ▴ 110
2
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4
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399
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Replace SB flag by PASS in my VCF file
VCF
4 months ago by ManuelDB ▴ 110
0
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0
replies
399
views
Comment: Comment: Replace SB flag by PASS in my VCF file
4 months ago by ManuelDB ▴ 110
2
votes
1
reply
236
views
GATK4 VariantAnnotator deletes variants
GATK4
updated 4 months ago by 164k • written 4 months ago by ▴ 110
0
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0
replies
202
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Understanding the transcript version comparison in the ncbi webside
NCBI
5 months ago by ManuelDB ▴ 110
0
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1
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529
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Comment: Comment: New versions of the same transcripts ID may have different exons coordinates??
5 months ago by ManuelDB ▴ 110
3
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4
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529
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New versions of the same transcripts ID may have different exons coordinates??
RefSeq
updated 5 months ago by 20k • written 5 months ago by ▴ 110
1
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1
reply
296
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How can I get the total list of RefSeq transcripts?
RefSeq
updated 5 months ago by 147k • written 5 months ago by ▴ 110
0
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1
reply
526
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Answer: Answer: Could not parse a VCF file when using bcftools annotate
5 months ago by ManuelDB ▴ 110
1
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3
replies
526
views
Could not parse a VCF file when using bcftools annotate
bcftools
updated 5 months ago by 44k • written 5 months ago by ▴ 110
1
vote
1
reply
274
views
Alternative Database for Somatic Indel Realignment (COSMIC Alternative)
COSMIC
updated 5 months ago by ▴ 290 • written 5 months ago by ▴ 110
0
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1
reply
338
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PEAR seems to have sense to me
PEAR
updated 8 months ago by 147k • written 8 months ago by ▴ 110
0
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0
replies
237
views
MultiGemini is not doing indel realignment, right?? Gemini does't work with single read?
MultiGemini
9 months ago by ManuelDB ▴ 110
0
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0
replies
903
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Comment: Comment: 1 Bioinformatician position in San Sebastian (Spain)
9 months ago by ManuelDB ▴ 110
0
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0
replies
333
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Comment: Comment: FastaAlternateReferenceMaker merges overlapping regions
9 months ago by ManuelDB ▴ 110
0
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1
reply
333
views
FastaAlternateReferenceMaker merges overlapping regions
FastaAlternateReferenceMaker
updated 9 months ago by 44k • written 9 months ago by ▴ 110
0
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0
replies
700
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Comment: Comment: CIGAR and query sequence lengths differ
11 months ago by ManuelDB ▴ 110
0
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0
replies
700
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Comment: Comment: CIGAR and query sequence lengths differ
11 months ago by ManuelDB ▴ 110
1
vote
3
replies
700
views
CIGAR and query sequence lengths differ
pysam samtools
11 months ago by ManuelDB ▴ 110
1
vote
1
reply
554
views
How to properly mock a (Pysam) read
pysam
updated 11 months ago by 101k • written 11 months ago by ▴ 110
2
votes
1
reply
561
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools softclip
updated 11 months ago by ▴ 340 • written 11 months ago by ▴ 110
1
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1
reply
409
views
Two identical reads in my bam files but with a different in CIGAR are mapped in a different location in IGV
pysam
12 months ago by ManuelDB ▴ 110
1
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0
replies
409
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Answer: Answer: Two identical reads in my bam files but with a different in CIGAR are mapped in
12 months ago by ManuelDB ▴ 110
0
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0
replies
1.3k
views
Comment: Comment: Different number of reads when converting data from FASTQ to BAM and CRAM to FAS
13 months ago by ManuelDB ▴ 110
0
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0
replies
1.3k
views
Comment: Comment: Different number of reads when converting data from FASTQ to BAM and CRAM to FAS
13 months ago by ManuelDB ▴ 110
0
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1
reply
1.3k
views
Comment: Comment: Different number of reads when converting data from FASTQ to BAM and CRAM to FAS
13 months ago by ManuelDB ▴ 110
0
votes
2
replies
1.3k
views
Comment: Comment: Different number of reads when converting data from FASTQ to BAM and CRAM to FAS
13 months ago by ManuelDB ▴ 110
0
votes
1
reply
1.3k
views
Comment: Comment: Different number of reads when converting data from FASTQ to BAM and CRAM to FAS
13 months ago by ManuelDB ▴ 110
5
votes
10
replies
1.3k
views
Different number of reads when converting data from FASTQ to BAM and CRAM to FASTQ
picard
13 months ago by ManuelDB ▴ 110
0
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0
replies
1.0k
views
Comment: Comment: FASTQ to BAM to CRAM to FASTQ
13 months ago by ManuelDB ▴ 110
0
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0
replies
41k
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Comment: Comment: installing samtools with conda - overcoming two common errors
13 months ago by ManuelDB ▴ 110
1
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0
replies
22k
views
Comment: Comment: How To Efficiently Sort A Fastq File By Entry Id?
13 months ago by ManuelDB ▴ 110
5
votes
4
replies
1.0k
views
FASTQ to BAM to CRAM to FASTQ
Samtools
13 months ago by ManuelDB ▴ 110
0
votes
4
replies
1.8k
views
Cannot read non-existent file: when executing MarkDuplicates in a script
GATK4
updated 13 months ago by • 0 • written 2.7 years ago by ▴ 110
0
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0
replies
321
views
ERROR::INVALID_ALIGNMENT_START Alignment start should be 0 because reference name = *.
Pysam ValidateSamFile
13 months ago by ManuelDB ▴ 110
0
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0
replies
747
views
Comment: Comment: How to deal with reads which CIGAR is [0-9]+S
13 months ago by ManuelDB ▴ 110
1
vote
3
replies
747
views
How to deal with reads which CIGAR is [0-9]+S
CIGAR ampliconclip
updated 13 months ago by ★ 1.4k • written 13 months ago by ▴ 110
0
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0
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1.9k
views
Comment: Comment: Liftover GRCh37 to hg38 1kg/GATK.
14 months ago by ManuelDB ▴ 110
6
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2
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1.9k
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Liftover GRCh37 to hg38 1kg/GATK.
Liftover
14 months ago by ManuelDB ▴ 110
0
votes
0
replies
880
views
Comment: Comment: samtools ampliconclip option --strand is not working?
14 months ago by ManuelDB ▴ 110
5
votes
2
replies
880
views
samtools ampliconclip option --strand is not working?
samtools ampliconclip
14 months ago by ManuelDB ▴ 110
1
vote
0
replies
1.2k
views
Comment: Comment: How is the format of the bed file for samtools ampliconclip
14 months ago by ManuelDB ▴ 110
0
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1
reply
1.2k
views
Comment: Comment: How is the format of the bed file for samtools ampliconclip
15 months ago by ManuelDB ▴ 110
4
votes
7
replies
1.2k
views
How is the format of the bed file for samtools ampliconclip
samtools ampliconclip
updated 14 months ago by ▴ 340 • written 15 months ago by ▴ 110
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