User: steven.davis

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steven.davis10
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2 years, 11 months ago
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Posts by steven.davis

<prev • 7 results • page 1 of 1 • next >
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VCF INFO AC field for failed snps
... What is the standard VCF INFO field, if any, to count the occurrences of variant genotypes having passed all filters? Does AC count every occurrence of the alternate genotype, or only those occurrences where the call passes all filters? Consider the haploid VCF snippet below. At position 300, the ...
vcf written 7 months ago by steven.davis10
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Answer: A: MAF to Fasta or XMFA - how does it work?
... @jrj.healey This is 15 months after your original post, but may help others. There is a maf2fasta.pl conversion script included with mugsy. How did you solve the conversion problem? ...
written 14 months ago by steven.davis10
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Comment: C: Parsing flowcell from hiseq 2000 read name
... Thank you Pierre. I'm writing a Python module to parse the sequence ids and extract various data elements. I will put it on GitHub sometime soon. ...
written 2.6 years ago by steven.davis10
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Comment: C: Illumina Instrument Type from fastq?
... What kind of instrument uses flowcells ending with BBXX? Here is the read sequence id line: @ERR1417747.1 K00150:65:H77FVBBXX:7:1101:1570:1297 length=150 ...
written 2.6 years ago by steven.davis10
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Parsing flowcell from hiseq 2000 read name
... Is there a way to extract instrument and flowcell from a read name like this: >gnl|SRA|SRR1840614.1.1 FCC1KPRACXX:1:1101:1291:2172 FCC1KPRACXX : what is this? 1 = lane? 1101 = ? 1291 = x 2172 = y I need to extract the flowcell if possible, so it can be assigned to reads ...
illumina fastq hiseq written 2.6 years ago by steven.davis10 • updated 2.6 years ago by Pierre Lindenbaum123k
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Answer: A: VCF output when merging with bcftools merge
... Solved it with help from a colleague. Problem solved with "--merge all" command line option. ...
written 2.9 years ago by steven.davis10
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VCF output when merging with bcftools merge
... I am merging multiple single-sample VCF files into one multi-sample VCF file with bcftools merge using this command: bcftools merge --info-rules NS:sum -o outFilePath dir/*.gz Previously, using bcftools 1.1, the output VCF file contained one row per position, like this: #CHROM POS ID ...
vcf bcftools written 2.9 years ago by steven.davis10

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For VCF output when merging with bcftools merge

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