Tag: QUAL

How good is Genozip at compressing BAM files? ​ See Benchmarks. ​ Compressing a BAM, SAM or CRAM file  ​ In the rest of this page we will give examples of BAM files. Genozip is also capable of compressing SAM files, and with some limitations, CRAM files as well. ​…

NAME SYNOPSIS DESCRIPTION EXAMPLES BASIC OPTIONS SITE FILTERING OPTIONS INDIVIDUAL FILTERING OPTIONS GENOTYPE FILTERING OPTIONS OUTPUT OPTIONS COMPARISON OPTIONS AUTHOR NAME VCFtools v0.1.12a − Utilities for the variant call format (VCF) and binary variant call format (BCF) SYNOPSIS vcftools [ –vcf FILE | –gzvcf FILE | –bcf FILE]…

Hi everyone, I am currently working on a medium-sized WES cohort study and wanted to know what the bioinformatics community would regard a cutting-edge workflow. As the big labs usually utilize GATK I also started with that. The results for SNPs are ok, but manual inspection (IGV) still uncovers a…

annotation_file ##INFO=<ID=ClinVar_CLNSIG,Number=.,xxx ##INFO=<ID=ClinVar_CLNREVSTAT,Number=.,yyy ##INFO=<ID=ClinVar_CLNDN,Number=.zzz #CHROM POS ID REF ALT QUAL FILTER INFO chr1 10145 . AAC A 101.83 . AC=2;AF=0.067;AN=30;aaa chr1 10146 . AC A 98.25 . AC=2;AF=0.083;AN=24;bbb chr1 10146 . AC * 79.25 . AC=2;AF=0.083;AN=24;ccc chr1 10439 . AC A 81.33 . AC=1;AF=0.008333;AN=120;ddd chr1 10450 . T G 53.09…

Newbie here. Please, play nice. I got possession of a set of 4 .bam files that stores the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with…

bowtie2 – (ERR): bowtie2-align exited with value 13 1 I am trying to run bowtie2. but following error are occuring everytime bowtie2 –very-fast-local -x bowtie -q -1 R1.fastq -2 R2.fastq -s aligned.sam Saw ASCII character 10 but expected 33-based Phred qual. terminate called after throwing an instance of ‘int’ Aborted…

Why did I achieve shorter than initial reads subset after aligned reads extraction. 1 Hello dear colleages! I have recently faced some problem. I have worked with long WGS reads. Firstly I have filtered the longest subset of reads, and aligned them to the custom sequence with several structural variants…

Provided by: sambamba_0.8.2+dfsg-2_amd64 NAME sambamba-view – tool for extracting information from SAM/BAM files SYNOPSIS sambamba view OPTIONS <input.bam | input.sam> [region1 […]] DESCRIPTION sambamba view allows to efficiently filter SAM/BAM files for alignments satisfying various conditions, as well as access its SAM header and information about reference sequences. In order…

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AllHigh-Throughput SequencingGenomicsProteomicsVisualizationOther BBTools Description a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. Installation Use the following command to…

I’m using Biopython to parse a fastq file, and I found that the SeqIO object get cleared away once I accessed it. from Bio import SeqIO record_fastqIO = SeqIO.parse(‘SRR835775_1.first1000.fastq’,’fastq’) for record in record_fastqIO: print(record.id) This script works perfectly. But if I add one line to the script: from Bio import…

Dear all, I have a particular vcf file like this, chrX 29 . G A,T . PASS AC=1,1;AN=3 GT:DP:HF:CILOW:CIUP:SDP 0/1/2:4839:0.003,0.001:0.002,0.0:0.005,0.003:14;0,4;2 I tried various tools to split this, but I get the following results, so the FORMAT and INFO lines are identical. chrX 29 . G A . PASS AC=1,1;AN=3;OLD_MULTIALLELIC=chrM:899:G/A/T GT:DP:HF:CILOW:CIUP:SDP…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…