Question: GATK haplotypecaller can be restricted to specific intervals using -L option, but can we add other information with interval files to the VCF?
gravatar for Hemant Gupta
3.1 years ago by
Hemant Gupta0 wrote:

Dear Biostars,

I have interval.list file with columns including chr, start, end, gene_name, TSS, Strand, as shown below:

chr19   58864565        58865165        A1BG                58864865        - 
chr19   58863035        58863635        A1BG-AS1            58863335        + 
chr10   52645135        52645735        A1CF                52645435        -

If any variant fall in to listed interval, How can I add gene name, TSS and Strand info relevant to that interval as well as variant to the VCF.


ADD COMMENTlink modified 3.1 years ago by Pierre Lindenbaum128k • written 3.1 years ago by Hemant Gupta0
gravatar for Pierre Lindenbaum
3.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

I don't think you can do this with GATK

I've writtern

$ tabix -h dbsnp138_00-All.vcf.gz "19:58864565-58865165" | sed '/^[^#]/s/^/chr/' |\
java -jar dist/vcfbed.jar -m your.bed -f '${1}|${2}|${3}|${4}&${5}'

##INFO=<ID=VCFBED,Number=.,Type=String,Description="metadata added from your.bed . Format was ${1}|${2}|${3}|${4}&${5}">
chr19   58864911    rs113760967 T   C   .   .   GNO;OTHERKG;R5;RS=113760967;RSPOS=58864911;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VP=0x050100020001000102000100;WGT=1;dbSNPBuildID=132
chr19   58865054    rs893183    T   C   .   .   CAF=[0.1299,0.8701];COMMON=1;G5;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;PH3;R5;RS=893183;RSPOS=58865054;RV;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VLD;VP=0x05010002000115051f000100;WGT=1;dbSNPBuildID=86
chr19   58865068    rs893182    T   C   .   .   CAF=[0.1299,0.8701];COMMON=1;G5;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;PH3;R5;RS=893182;RSPOS=58865068;RV;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VLD;VP=0x05010002000115051f000100;WGT=1;dbSNPBuildID=86
chr19   58865082    rs893181    A   T   .   .   CAF=[0.1295,0.8705];COMMON=1;G5;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;PH3;R5;RS=893181;RSPOS=58865082;RV;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VLD;VP=0x05010002000115051f000100;WGT=1;dbSNPBuildID=86
chr19   58865091    rs893180    A   G   .   .   CAF=[0.1299,0.8701];COMMON=1;G5;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;R5;RS=893180;RSPOS=58865091;RV;SAO=0;SLO;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VLD;VP=0x05010002000115051e000100;WGT=1;dbSNPBuildID=86
chr19   58865112    rs188818621 C   T   .   .   CAF=[0.9954,0.004591];COMMON=1;KGPROD;KGPhase1;R5;RS=188818621;RSPOS=58865112;SAO=0;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VP=0x050000020001000014000100;WGT=1;dbSNPBuildID=135
chr19   58865164    rs80109863  C   T   .   .   CAF=[0.9949,0.005051];COMMON=1;GNO;KGPROD;KGPhase1;OTHERKG;R5;RS=80109863;RSPOS=58865164;SAO=0;SSR=0;VC=SNV;VCFBED=chr19|58864565|58865165|A1BG&58864865;VP=0x050000020001000116000100;WGT=1;dbSNPBuildID=132

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Pierre Lindenbaum128k

I got following error while compiling your program:

cp --verbose "/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcfbed/" "/jvarkit/_tmp-2.9.1/com/github/lindenb/jvarkit/tools/vcfbed/"
cp: illegal option -- -
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
       cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory
make: *** [vcfbed] Error 64

is there any workaroud to solve this problem, I think its conflicting with MacOS build.

ADD REPLYlink written 3.1 years ago by Hemant Gupta0

But it works on Linux and the output is like what i want, Thanks alot!

ADD REPLYlink written 3.1 years ago by Hemant Gupta0

good to know, Thanks , I've changed the option --verbose to -v in my Makefile.

ADD REPLYlink written 3.1 years ago by Pierre Lindenbaum128k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1951 users visited in the last hour