User: agathejouet

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Posts by agathejouet

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Comment: C: filter multisample vcf based on per-sample average read depth
... First sentence is correct. However, I would like to compare the sample DP (in format field) to the average read depth of the sample overall. What would be good would be to have one file with the average read depth for all samples, e.g.: sample_ID avg_read_depth sample 1 100 ...
written 6 months ago by agathejouet0
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Consensus sequences with reference allele instead of missing
... Hi all, I am trying to use `bcftools consensus` (version 1.3.1) to get consensus sequences using a reference fasta file and a multisample vcf. The problem is that when bases are missing (I can actually see that on my bam files), `bcftools consensus` prints the reference allele. I would like to ha ...
consensus missing bases bcftools written 6 months ago by agathejouet0
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Comment: C: filter multisample vcf based on per-sample average read depth
... Can I have a bit more information on how your script works Pierre, please? From what I can guess, it changes alternate alleles to reference alleles when read depth at the SNP is larger than double the average read depth across samples. Is that right? However what I would need is to filter according ...
written 6 months ago by agathejouet0
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Comment: C: filter multisample vcf based on per-sample average read depth
... Not sure this is what you want but my multisample vcf looks like this at the moment: LOC_Os01g02250_chr1_688792..693013_UTR-0 1422 . A G 999 . . GT:PL:DP 1/1:245,247,0:82 1/1:217,211,0:70 1/1:242,255,0:144 1/1:234,234,0:84 ...
written 6 months ago by agathejouet0
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Comment: C: filter multisample vcf based on per-sample average read depth
... Yes, I thought of re-doing the variant calling for each individual separately and merging the resulting vcf files. The problem with this is that samples that were homozygous for the reference alleles will end up with missing genotypes if other individuals were variant. A way around this would be to ...
written 6 months ago by agathejouet0
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Comment: C: filter multisample vcf based on per-sample average read depth
... That is exactly my problem. The average read depth is different for each sample so I would need to find a way to modify the genotypes of each sample individually. My ultimate goal is to have a VCF file with all samples, where SNPs have been filtered for a minimum and a maximum read depth. I would us ...
written 6 months ago by agathejouet0
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filter multisample vcf based on per-sample average read depth
... Hi, I have a multisample vcf that I would like to filter based on read depth. More precisely, I would like to modify the vcf so that a snp that is detected where the read depth is more than the average read depth at the sample will change to the reference allele. I know how to filter snps where rea ...
vcf filter variant call read depth written 6 months ago by agathejouet0 • updated 6 months ago by Pierre Lindenbaum108k
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Comment: C: bcftools merge, error "Could not parse the region(s)"
... Thanks very much for your help, will try to modify this! Agathe ...
written 8 months ago by agathejouet0
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Comment: C: bcftools merge, error "Could not parse the region(s)"
... The output is: LOC_Os01g16370_chr1:9292171..9298764_UTR-0 LOC_Os01g16400_chr1:9313135..9317036_UTR-0 LOC_Os01g21240_chr1:11854526..11857948_UTR-0 LOC_Os01g25630_chr1:14525576..14530578_UTR-0 LOC_Os01g25710_chr1:14570811..14580124_UTR-0 LOC_Os01g25810_chr1:14611521..14616096_ ...
written 8 months ago by agathejouet0
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bcftools merge, error "Could not parse the region(s)"
... Hi all, I am trying to merge multiple vcf files using bcftools version 1.6. Unfortunately, I receive the following error for all of my "chromosomes": [E::_regions_init_string] Could not parse the region(s): chr1 ex: [E::_regions_init_string] Could not parse the region(s): JA218_chr6:299 ...
vcf merge bcftools tabix written 8 months ago by agathejouet0 • updated 8 months ago by Pierre Lindenbaum108k

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