GATK haplotypecaller can be restricted to specific intervals using -L option, but can we add other information with interval files to the VCF?

Question

[Hemant Gupta]

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.

Thanks,

Answer 1

[Pierre Lindenbaum]

I don't think you can do this with GATK

I've writtern https://github.com/lindenb/jvarkit/wiki/VCFBed

$ 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

[Hemant Gupta]

I got following error while compiling your program:

cp --verbose "/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcfbed/VCFBed.java" "/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.

[Hemant Gupta]

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

[Pierre Lindenbaum]

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