User: Pierre Lindenbaum

... create the following '**Makefile**' SHELL=/bin/bash BAMS=$(shell ls -1 *.bam) define run $$(addsuffix .sorted.bam,$$(basename $(1))): $(1) samtools sort $$< $$(basename $$@) samtools index $$@ endef all: $(addsuffix .sorted.bam,$(basename ${BAMS})) ...

written 1 day ago by Pierre Lindenbaum ♦ 95k

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Comment: C: bbnorm Java error?

... I was asking for the version of bbnorm ...

written 2 days ago by Pierre Lindenbaum ♦ 95k

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107

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Comment: C: bbnorm Java error?

... which version is it ? ...

written 2 days ago by Pierre Lindenbaum ♦ 95k

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135

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Comment: C: tabix for ID column

... yes because join optimize the fact that the file is sorted: it will ignore everything before rs1234 and stop after rs1234. of course , for speed you would use: LC_ALL=C grep -w '^rs1234' but you don't know is there is more than one occurence of rs1234 in the file (it happens) grep -w - ...

written 2 days ago by Pierre Lindenbaum ♦ 95k

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Answer: A: tabix for ID column

... create a text file filled with `RSID CHROM POS` and sort on RSID. awk '/^#/ {next;} ($3==".") {next;} {OFS="\t";print $3,$1,$2;}' input.vcf | sort -k1,1 > index.txt when querying , use **join** build an interval and query with tabix join -t $'\t' -1 1 -2 1 <(echo "rs12345") i ...

written 2 days ago by Pierre Lindenbaum ♦ 95k

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Comment: C: Same samples, different IDs, merge two VCFs

... did you try vcftools or gatk to merge your vcfs ? ...

written 3 days ago by Pierre Lindenbaum ♦ 95k

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203

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Answer: A: How to generate alignment report from bam files

... I've written : FindAllCoverageAtPosition http://lindenb.github.io/jvarkit/FindAllCoverageAtPosition.html it reports the coverage+bases (not shown in the html doc)+cigar-operators at a given position for a set of files: $ find ./ -type f -name "*.bam" |\ java -jar dist/findallcoverageat ...

written 3 days ago by Pierre Lindenbaum ♦ 95k

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Comment: C: In Silico Genome Digestion ?

... > This java script for in silico restriction digestion does not do reverse complementary search, am I right ? https://en.wikipedia.org/wiki/Palindromic_sequence#Restriction_enzyme_sites ...

written 3 days ago by Pierre Lindenbaum ♦ 95k

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108

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Comment: C: Barriers to a clinical "Test Once, Analyze Many" molecular DNA strategy.

... EHR: Electronic Health Record ...

written 3 days ago by Pierre Lindenbaum ♦ 95k

Latest awards to Pierre Lindenbaum

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi

Scholar 2 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs

Appreciated 2 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org

Scholar 2 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi

Student 3 days ago, asked a question with at least 3 up-votes. For Exome Aggregation Consortium (ExAC) database ?

Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi

Appreciated 3 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi

Scholar 3 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs

Appreciated 4 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org

Popular Question 5 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi

Scholar 6 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs

Appreciated 9 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi

Scholar 10 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs

Appreciated 10 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi

Scholar 12 days ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Poly A Sequences In Small Rna

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