Admin: Pierre Lindenbaum
Pierre Lindenbaum ♦ 94k
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Posts by Pierre Lindenbaum
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... curl -s "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" | gunzip -c | grep "EX_TARGET" -m1
##INFO=
> indicates whether a variant is within the exon pull down target boundaries ...
written 1 day ago by
Pierre Lindenbaum ♦ 94k
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... Hello zengxi.hada!
We believe that this post does not fit the main topic of this site.
not related to bioinformatics. ask https://academia.stackexchange.com/
For this reason we have closed your question. This allows us to keep the site focused
on the topics that the community can help with.
...
written 3 days ago by
Pierre Lindenbaum ♦ 94k
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... > Given the positions of the SNPs in the contigs of the alignment,
what is this file ? does it contains CHROM and POS ?
> I'm now trying to plot the distribution of found variants along each chromosome.
if so, why do you need the other steps ? Mummer3 etc... ? ...
written 3 days ago by
Pierre Lindenbaum ♦ 94k
4
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... * using **awk** get the chrom/start of the VCF, group the pos by windows of 10000
* **sort** / **uniq** to get the count of variants in each window of 10000 bp
* use awk to create chrom/start/end/count . The chrom must be the same than in the circos karyotype/config, that's with I why I've added a ' ...
written 3 days ago by
Pierre Lindenbaum ♦ 94k
0
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2
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162
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... histogram of what ? variant per Mb ? per sample/genotypes Mb ?
...
written 4 days ago by
Pierre Lindenbaum ♦ 94k
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61
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... and what is this ENGXXXXX1 ? I cannot see this in your URL ...
written 4 days ago by
Pierre Lindenbaum ♦ 94k
0
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1
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75
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1
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Answer:
A: where is latest omim.txt.Z?
... OMIM is no longer part of the NCBI.
see https://www.omim.org/
I'm not even sure, this file omim.txt.Z is still generated: https://omim.org/downloads/
...
written 5 days ago by
Pierre Lindenbaum ♦ 94k
0
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61
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... > the BioPAX format is not quite straight forward to process.
where is this file please ? ...
written 5 days ago by
Pierre Lindenbaum ♦ 94k
0
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2
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191
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2
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... please check the green marks on the left to validate+close the question ...
written 6 days ago by
Pierre Lindenbaum ♦ 94k
1
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... using sam2tsv : http://lindenb.github.io/jvarkit/Sam2Tsv.html
$ java -jar dist/sam2tsv.jar ~/scf7180000354095.bam -R ~/scf_7180000354095.fasta
#READ_NAME FLAG CHROM READ_POS BASE QUAL REF_POS REF OP
HISEQ:348:H2YWCBCXX:1:1115:19355:8 ...
written 6 days ago by
Pierre Lindenbaum ♦ 94k
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