Tag: QUAL

bedtools intersect error: Invalid record in file

Hello to all I am trying to run bedtools intersect with vcf file and a bed file (my goal is to add the depth data to my VCF) I get an error running this command: bedtools intersect -a depth.bed -b fish.vcf -wa -wb > $out The error: “Error: Invalid record…

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Issue with fastq after converting phred 64 to phred 33 quality scores

Hello, I ran seqtk seq -VQ64 read1.fastq.gz > read1_phred33.fastq to convert my 64 based phred score reads to 33 based phred score phred reads. However when I attempted to run them through tophat alignment I got this error: Saw ASCII character 4 but expected 33-based Phred qual. terminate called after…

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Dragen-gatk for trio

Dragen-gatk for trio 0 Hi everyone, the Dragen gatk pipeline works great for single sample. however I would like to know if any have used this pipeline for a trio? if so how did you do it? it is recommended to do a hard filtering based on QUAL but how…

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how to add reference alleles to VCF?

how to add reference alleles to VCF? 1 I’m converting gVCFs to VCF, but the reference alleles are missing. An example below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 180525_FD02929177 1 97547947 . T . . . DP=31 GT:DP:RGQ 0/0:31:81 1 97915614 . C . . . DP=40…

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No quality in non-variant sites GATK

No quality in non-variant sites GATK 1 Heys, I am doing the SNP calling with Haplotypecaller BP_Resolution, CombineGVCFs with convert-to-base-pair-resolution and GenotypeGVCFs with include-non-variant-sites with GATK and when I get my vcf file, the non-variant sites does not have any quality at all: #CHROM POS ID REF ALT QUAL FILTER…

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VCF samtools

VCF samtools 0 Hello, I am having trouble when doing variant calling with samtools. I am getting only the header an no variants. If I would instead use Freebayes, I do get a lot of variables, and with Gatk, I get just a few. What can the problem be? Do…

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add gene names to ‘isec’ output files of bcftools’

add gene names to ‘isec’ output files of bcftools’ 1 I had two vcf files and I used isec from bcftools software to find typical and common mutations between samples. The output of isec function were four vcf.gz file showing like below: isec_output/0000.vcf.gz would be variants unique to 1.vcf.gz isec_output/0001.vcf.gz…

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I can’t get a dossage file using PLINK

Hi, I have been trying to get a dosage file from vcf, map and fam files. For that, I have written this bash script : plink –fam plink.fam –map plink.map –dosage one.vcf –write-dosage However, I got this error: –dosage: Reading from one.vcf. Error: Line 1 of one.vcf has fewer tokens…

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vcf to bgen conversion using qctool v2 yields 0 snps

Hi all, I have a vcf file that was extracted from UKB data using qctool (v2.0.6-Ubuntu16.04-x86_64) and contains data in the GP format. This contains a bunch of SNPs from a single chromosome. ❱ wc -l chromosome1.vcf 260 chromosome1.vcf Then I try to convert this file to .bgen again using…

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predixcan error

predixcan error 0 Hello, I am trying to run predict.py script from predixcan software But its showing error for me. The command use: python $PXCN_TOOLS/PrediXcan.py –model_db_path $MODELS/en_Whole_Blood.db –model_db_snp_key rsid –vcf_mode genotyped –vcf_genotypes $VCF_FILES/*.vcf –prediction_output $OUTPUT/GVDS_PrediXcan_Test_2021.txt the error: [E::bcf_hdr_parse] Could not parse the header, sample line not found Segmentation fault I…

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bcftools merge

Check out the vcf_merge command I wrote: $ fuc vcf_merge -h usage: fuc vcf_merge [-h] [–how TEXT] [–format TEXT] [–sort] [–collapse] vcf_files [vcf_files …] This command will merge multiple VCF files (both zipped and unzipped). It essentially wraps the ‘pyvcf.merge’ method from the fuc API. By default, only the GT…

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Edit vcf file 0|0 to 0

Edit vcf file 0|0 to 0 1 I have a vcf file with GT format as 0|0 0|1 1|1 etc. I would like to convert those to a single number to create a dosage file. Ex: Editing the vcf so that 0|0 become 0, 0|1 becomes 1 1|1 becomes 2…

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Output of samtools view, what does the third column actually represent?

The samtools view outputs information from SAM and BAM files in SAM format. You can find a description of the SAM format here: samtools.github.io/hts-specs/SAMv1.pdf Section 1.4 deals with the meaning of each of the manditory coloumns. It includes the following table: Col Field Type Regexp/Range Brief description |—|——|——-|—————————-|—————————————-| 1 QNAME…

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Extract multiple times a fasta sequence from a list by name

Hi everybody! I have uploaded on R a list of 9K fasta sequences, on which 40K SNPs map to – which means, some sequence host 1+ SNP. I have a R object (and a vcf as well) with the fasta sequences names and the SNP positions and I want to…

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bcftools merge; retaining sample names

bcftools merge; retaining sample names 2 When I do bcftools merge, the headers do not retain the filenames.  How can I specify filenames? This is my command  bcftools merge vcf/unfiltered/*.vcf.gz -O z > msa/pooled.vcf.gz However this is the relevant part of my header, despite the filenames I gave it.  Is…

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Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )

Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles ) 1 I’m trying to achieve what this post was looking for Add Dp Tag To Genotype Field Of Vcf File Currently this is my command: bcftools mpileup -Ou –max-depth 8000 –min-MQ…

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FreeBayes VCF output with FORMAT unknown

Hey, I am looking for a way to add samples ID names to the FORMAT in my vcf file. I have 10 sorted Bam files. I used Freebayes to create vcf files and my next step is merging all 10 files for VcfSampleCompare. And for that I need to define…

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Change chromosome notation in dbSNP VCF file

Change chromosome notation in dbSNP VCF file 0 Hiii, I have downloaded dbSNP VCf file from [ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/] The format is as follows: #CHROM POS ID REF ALT QUAL FILTER INFO 1 10019 rs775809821 TA T . . RS=775809821;RSPOS=10020;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000020005000002000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP 1 10039 rs978760828 A C . . RS=978760828;RSPOS=10039;dbSNPBuildID=150;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP 1 10043 rs1008829651 T…

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Convert a VCF-file in a user specific Format

Convert a VCF-file in a user specific Format 0 Hello everyone, I am curious if it is possible to convert a VCF-File (with multiple samples) in a Format whith 5 columns. Column should be Sample ID Column: Position on the chromosome Genotyp Number of reads covering site QUAL phred-scaled quality…

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Platypus

Platypus 0 Hi, I’m super new to WGS and bioinformatics, but I’m a classic software data scientist, so I know enough to be annoying. I’m using Platypus too call variants on 100X WGS via Nebula Genomics. I found an odd series of calls and am not sure if this is…

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Variant Calling Heterozygous Reference Alleles

I am going to be working with VCF files a lot in the near future so I thought I would brush up on the practice. After much reading and research, there’s something that I just can’t wrap my head around. 1) In a diploid organism, you have 2 alleles for…

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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print only columns with data from every line

print only columns with data from every line 0 Hi, I have a vcf file where is about 60 000 columns. Here is example of the first three lines: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 10022-20416-17 10024-34469-18A 10025-34469-18B 10034-31625-18A 10035-31625-18B 10036-31625-18C 10042-29083-18 10044-34485-18A 10045-34485-18B 10046-34485-18C 10069-33802-18 10070-20895-17…

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bcftools consensus still returns “Could not parse the header” error

bcftools consensus still returns “Could not parse the header” error 0 I attempted to create a consensus fasta file using bcftools, i.e. bgzip -c All_SRR_SNP_Clean.vcf > All_SRR_SNP_Clean.vcf.gz tabix All_SRR_SNP_Clean.vcf.gz cat $ref| bcftools consensus $vcf_dir/All_SRR_SNP_Clean.vcf.gz > consensus.fasta where $ref is the path to a Drosophila reference genome fa and the vcf…

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VCF Filter On Small Genomes

VCF Filter On Small Genomes 0 Hi guys, I am working on a yeast species (Candida glabrata) NGS data to find any mutations related to drug resistance. I am new in bioinformatics so I am using Galaxy.eu to get use to algorithms. There is literature about some genes that mutations…

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