Tag: VDB

links to Ensembl GRCh37 – gitmetadata

Open Targets Genetics reports GRCh38 coordinates but ‘External references” section points to GRCh37 (grch37.ensembl.org) rather than GRCh38 (www.ensembl.org): genetics.opentargets.org/variant/8_102432699_T_C Was this a deliberate decision (e.g. we don’t have the rsID in GRCh38 for some reason, other)? If so, we need to make this clear in the docs. If not, we…

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How to call variant by –max-depth for RNAseq

Hi everyone! I have a query regarding variant calling from a high coverage site on the basis of the maximum likelihood variant. I have RNA-seq data mapped bam file. I called variant using the below command. “bcftools mpileup –max-depth 10000 -Oz -f ref.fa sample.bam | bcftools call -mv -Oz -o…

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bcftools merge GP format issues

Hello, I am trying to merge VCF files from several samples from different sequencing runs. I ran bcftools merge on the VCF files and after ten hours I got the error message “Incorrect number of FORMAT/GP values at chr_Y:216795, cannot merge. The tag is defined as Number=G, but found 2…

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converting SAM file to SRA

converting SAM file to SRA 0 Does Anybody know how to convert SAM files to equivalent SRA ? I downloaded a SRA file and used sam-dump to convert it to sam format. Thereafter, I used bam-load to convert sam file to SRA. The reference fasta and configuration files are specified…

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Downloading authorized data from dbGAP leads to a “looped” message

Downloading authorized data from dbGAP leads to a “looped” message 0 Hello everyone, i am trying to download authorized dbGAP data. My PI gave me the .ngc key and the necessary kart file. I used this as a guide to configure vdb-config: github.com/ncbi/sra-tools/wiki/05.-Toolkit-Configuration I then tried to use prefetch to…

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SRA Toolkit Error while using prefetch

SRA Toolkit Error while using prefetch 1 After installing SRA-toolkit I downloaded an SRA file and when I tried to download another SRA file then it gave me the following error: prefetch:` symbol lookup error: /lib/x86_64-linux-gnu/libncbi-vdb.so.2: undefined symbol: vdb_mbedtls_md_setup How to fix this? sra-toolkit • 20 views • link •…

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blastn_vdb Error: Cannot open VDB:

blastn_vdb Error: Cannot open VDB: 0 I’m working locally with sra-toolkit. I have downloaded a sra files, validate it with vdb-validate and when I try to do a search with blastn-dbd the following error occurs Error: Cannot get VDB column: ./SRR7443983.sra.SEQUENCE.ACC_PREFIX Anyone knows how to fix it? Thanks blastn_vdb •…

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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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VcfSampleCompare – empty output with warnings

Hello to all, I have 10 vcf files – 5 female fish and 5 male fish, I have merged all 10 fish to one vcf file.(all_fish.vcf) I performed the VcfSampleCompare analysis on ‘all_fish.vcf’ , following this:github.com/hepcat72/vcfSampleCompare The example command : vcfSampleCompare.pl –sample-group ‘wt1 wt2 wt3’ –sample-group ‘mut1 mut2 mut3’ input.vcf…

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