BaseRecalibrator - no suitable codecs
Answered
Can you please provide
a) GATK version use: 4.1.4.1
b) Exact GATK commands used
c) The entire error log if applicable.
Hi Team
I'm fairly new to GATK and very new to posting on here so apologies in advance
I'm having a problem getting BaseRecalibrator function to work for me using input RNA seq data in bam format that has been through splitntrim as per workflow. I am using vcf 00-All.vcf(.gz) downloaded from https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/#table-1
I keeping getting "a no suitable codecs problem"
I found a post from April 2017 with same error but alas have not been able to get this working
Error in full:
Command line:
gatk BaseRecalibrator -I /users/rlsmith/sharedscratch/split/RA003_split.bam -R genome.fa --known-sites /mnt/lustre/users/hlwright/00-All.vcf.tbi -O RA003_recal.table
Currently Loaded Modulefiles:
1) apps/star/2.7.3a
Using GATK jar /mnt/data1/users/software/GATK/gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /mnt/data1/users/software/GATK/gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar BaseRecalibrator -I /users/rlsmith/sharedscratch/split/RA003_split.bam -R genome.fa --known-sites 00-All.vcf.tbi -O RA003_recal.table
10:56:24.194 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/data1/users/software/GATK/gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 01, 2020 10:56:24 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:56:24.544 INFO BaseRecalibrator - ------------------------------------------------------------
10:56:24.545 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.4.1
10:56:24.545 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
10:56:24.546 INFO BaseRecalibrator - Executing as rlsmith@node062.pri.barkla.alces.network on Linux v3.10.0-1062.9.1.el7.x86_64 amd64
10:56:24.546 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_232-b09
10:56:24.546 INFO BaseRecalibrator - Start Date/Time: 01 April 2020 10:56:23 BST
10:56:24.546 INFO BaseRecalibrator - ------------------------------------------------------------
10:56:24.546 INFO BaseRecalibrator - ------------------------------------------------------------
10:56:24.547 INFO BaseRecalibrator - HTSJDK Version: 2.21.0
10:56:24.547 INFO BaseRecalibrator - Picard Version: 2.21.2
10:56:24.547 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:56:24.547 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:56:24.547 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:56:24.547 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:56:24.547 INFO BaseRecalibrator - Deflater: IntelDeflater
10:56:24.547 INFO BaseRecalibrator - Inflater: IntelInflater
10:56:24.547 INFO BaseRecalibrator - GCS max retries/reopens: 20
10:56:24.547 INFO BaseRecalibrator - Requester pays: disabled
10:56:24.547 INFO BaseRecalibrator - Initializing engine
10:56:25.131 INFO BaseRecalibrator - Shutting down engine
[01 April 2020 10:56:25 BST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2216165376
***********************************************************************
A USER ERROR has occurred: Cannot read file:///mnt/lustre/users/rlsmith/hg38/Bowtie2Index/00-All.vcf.tbi because no suitable codecs found
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
******
I have tried running both the zipped and unzipped, and have tried indexing and running the .tbi file with no luck
If I run the vcf (un indexed) then iI get the error: A USER ERROR has occurred: Input /mnt/lustre/users/hlwright/00-All.vcf must support random access to enable queries by interval. If it's a file, please index it using the bundled tool IndexFeatureFile
Any help to advise me on my errors would be much appreciated
With thanks
-
Hi,
The input for knownsites argument should be a vcf file and you are providing it a vcf-index file. Take a look at the tools docs: https://gatk.broadinstitute.org/hc/en-us/articles/360041850511-BaseRecalibrator
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Hi Bhanu
Thanks for your reply
I think I initially got errors with my vcf file as it was in a different folder to my index file and that was the problem. I then started using the index files as you identified. I have now got it working. Many thanks for your time and help
Best wishes
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hi ,when i use ~/software/gatk-4.2.0.0/gatk FastaAlternateReferenceMaker -R chr1.fa -O chr1gatk.fasta -V variations.vcf.idx to build myown reference fasta file, I meet an error like this:
A USER ERROR has occurred: Cannot read file:///data/zhangmr/peng/modifref/variations.vcf.idx because no suitable codecs found
the full log is here:
Using GATK jar /home/zhangmr/software/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/zhangmr/software/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar FastaAlternateReferenceMaker -R chr1.fa -O chr1gatk.fasta -V /data/zhangmr/peng/modifref/variations.vcf.idx
10:34:28.181 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/zhangmr/software/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 15, 2021 10:34:35 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:34:35.402 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
10:34:35.403 INFO FastaAlternateReferenceMaker - The Genome Analysis Toolkit (GATK) v4.2.0.0
10:34:35.403 INFO FastaAlternateReferenceMaker - For support and documentation go to https://software.broadinstitute.org/gatk/
10:34:35.403 INFO FastaAlternateReferenceMaker - Executing as zhangmr@centaur on Linux v4.15.0-128-generic amd64
10:34:35.403 INFO FastaAlternateReferenceMaker - Java runtime: OpenJDK 64-Bit Server VM v11.0.10+9-Ubuntu-0ubuntu1.18.04
10:34:35.404 INFO FastaAlternateReferenceMaker - Start Date/Time: April 15, 2021 at 10:34:28 AM CST
10:34:35.404 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
10:34:35.404 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Version: 2.24.0
10:34:35.405 INFO FastaAlternateReferenceMaker - Picard Version: 2.25.0
10:34:35.405 INFO FastaAlternateReferenceMaker - Built for Spark Version: 2.4.5
10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:34:35.405 INFO FastaAlternateReferenceMaker - Deflater: IntelDeflater
10:34:35.405 INFO FastaAlternateReferenceMaker - Inflater: IntelInflater
10:34:35.406 INFO FastaAlternateReferenceMaker - GCS max retries/reopens: 20
10:34:35.406 INFO FastaAlternateReferenceMaker - Requester pays: disabled
10:34:35.406 INFO FastaAlternateReferenceMaker - Initializing engine
10:34:35.567 INFO FastaAlternateReferenceMaker - Shutting down engine
[April 15, 2021 at 10:34:35 AM CST] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=2155872256
***********************************************************************A USER ERROR has occurred: Cannot read file:///data/zhangmr/peng/modifref/variations.vcf.idx because no suitable codecs found
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.could you help me to sovle this problem?
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Hi Miaoran ZHANG,
It looks like this error is coming from a file format issue. Here are the tool docs for that tool: FastaAlternateReferenceMaker. The tool needs a VCF input for the -V argument, and you are submitting an index file (/data/zhangmr/peng/modifref/variations.vcf.idx) instead of the VCF file.
Hope this helps!
Genevieve
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ey, ı am facing the same error and can't figure it out away.
A USER ERROR has occurred: Cannot read file:///mnt/e/thesis/data/hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz because no suitable codecs found
ı have all there reference related files that ı have installed from resource bundle
hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
hg38_v0_Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
hg38_v0_Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi hg38_v0_hapmap_3.3.hg38.vcf
hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf hg38_v0_hapmap_3.3.hg38.vcf.gz.tbi
hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz hg38_v0_wgs_calling_regions.hg38.interval_list hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.idx hg38_v0_Homo_sapiens_assembly38.dict
hg38_v0_Homo_sapiens_assembly38.fasta
hg38_v0_Homo_sapiens_assembly38.fasta.64.alt
hg38_v0_Homo_sapiens_assembly38.fasta.64.amb
hg38_v0_Homo_sapiens_assembly38.fasta.64.ann
hg38_v0_Homo_sapiens_assembly38.fasta.64.bwt
hg38_v0_Homo_sapiens_assembly38.fasta.64.pac hg38_v0_1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf hg38_v0_Homo_sapiens_assembly38.fasta.64.sa hg38_v0_1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf.idx hg38_v0_Homo_sapiens_assembly38.fasta.fai hg38_v0_1000G_omni2.5.hg38.vcf hg38_v0_Homo_sapiens_assembly38.known_indels.vcf hg38_v0_1000G_omni2.5.hg38.vcf.gz.tbi hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz.tbi hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf
ı used the bgzip command to convert my vcf files to vcf.gz as it is the proper way.
but still, ı'm facing the same error.
the command that ı run is;
gatk BaseRecalibrator \
-I mySample68snc.bam \
-R hg38_v0_Homo_sapiens_assembly38.fasta \
--known-sites hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz \
--known-sites hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz \
--known-sites hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz \
--known-sites hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
-O recal_data1.table
so if you have a suggestion ıt would make me so happy. Thank you...
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Hi Ekin Köni,
This error typically indicates that the input file is not being recognized properly as a vcf file. Could you try running "gzcat vcf | head -1" for the file that is causing the issue and paste the header line here? (example "##fileformat=VCFv4.2").
Kind regards,
Pamela
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##fileformat=VCFv4.1
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Ekin Köni, okay thank you for providing this. What version of GATK are you using?
-
The Genome Analysis Toolkit (GATK) v4.2.3.0
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Hi Ekin Köni,
Thank you. It's possible that there is an issue with how this file was compressed, causing it to be malformed. Could you try running PrintBGZFBlockInformation on the file? If there is an error, you may need to retry running bgzip on the vcf.
Kind regards,
Pamela
-
ı will try this suggestion thank you.
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Hello! I am receiving the exact error with the file: hg19_v0_Homo_sapiens_assembly19.dbsnp138.vcf
Please help:)
ref_snps='./reference_genome/hg19_v0_Homo_sapiens_assembly19.dbsnp138.vcf'
ref_indels='./reference_genome/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf'
ref='./reference_genome/hg19_v0_Homo_sapiens_assembly19.fasta'
#..more lines with code..
./gatk BaseRecalibrator \
-I $bam_marked_dup \
-R $ref \
--known-sites $ref_snps \
--known-sites $ref_indels \
-O $recal_table \
# ..result..
A USER ERROR has occurred: Cannot read file:///home/user/gatk_project/gatk-4.2.5.0/./reference_genome/hg19_v0_Homo_sapiens_assembly19.dbsnp138.vcf because no suitable codecs found -
Ekin Köni, do you have any suggestions that might help out Rea Kalampaliki?
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Rea Kalampaliki if you are still having issues with this file, go ahead and make a new post so we can walk you through the troubleshooting steps.
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I get the same error and do not seem to know whats wrong.
Using GATK jar /home/hi/Documents/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/hi/Documents/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar BaseRecalibrator -I /home/hi/Documents/bam_reads/file_copy_sorted.bam -R /home/hi/Documents/data/ref/hg38.fa --known-sites /home/hi/Documents/data/ref/Mills_and_1000G_gold_standard.indels.hg38.vcf -O /home/hi/Documents/data/sorted_ModyRead1.table
04:16:30.217 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/hi/Documents/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
04:16:30.446 INFO BaseRecalibrator - ------------------------------------------------------------
04:16:30.451 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.4.0.0
04:16:30.459 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
04:16:30.459 INFO BaseRecalibrator - Executing as oshi@oshi-VirtualBox on Linux v5.15.0-86-generic amd64
04:16:30.459 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.8.1+1-Ubuntu-0ubuntu120.04
04:16:30.460 INFO BaseRecalibrator - Start Date/Time: October 19, 2023 at 4:16:30 AM IST
04:16:30.460 INFO BaseRecalibrator - ------------------------------------------------------------
04:16:30.460 INFO BaseRecalibrator - ------------------------------------------------------------
04:16:30.463 INFO BaseRecalibrator - HTSJDK Version: 3.0.5
04:16:30.464 INFO BaseRecalibrator - Picard Version: 3.0.0
04:16:30.471 INFO BaseRecalibrator - Built for Spark Version: 3.3.1
04:16:30.472 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
04:16:30.480 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
04:16:30.495 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
04:16:30.495 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
04:16:30.496 INFO BaseRecalibrator - Deflater: IntelDeflater
04:16:30.497 INFO BaseRecalibrator - Inflater: IntelInflater
04:16:30.498 INFO BaseRecalibrator - GCS max retries/reopens: 20
04:16:30.498 INFO BaseRecalibrator - Requester pays: disabled
04:16:30.499 INFO BaseRecalibrator - Initializing engine
04:16:31.464 INFO BaseRecalibrator - Shutting down engine
[October 19, 2023 at 4:16:31 AM IST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=63025152
***********************************************************************A USER ERROR has occurred: Cannot read file:///home/hi/Documents/data/ref/Mills_and_1000G_gold_standard.indels.hg38.vcf because no suitable codecs found
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.please help if possible. thank you
-
Can you check the contents of the file
/home/hi/Documents/data/ref/Mills_and_1000G_gold_standard.indels.hg38.vcf
with bcftools view? It is possible that the file is corrupt or it may be empty.
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Hello, I'm currently trying to gatk IndexFeatureFile my vcf file, but it reported A USER ERROR has occurred: Cannot read file filtered_knownsites.vcf because no suitable codecs found.
When I cat filtered_knownsites.vcf | head -100, the following output shows:
chr1 8615 rs202245468 CCT C . PASS CAF=[0.9766,0.02342];COMMON=1;KGPROD;KGPhase1;KGPilot123;RS=202245468;RSPOS=233587;SAO=0;SSR=0;VC=DIV;VP=0x05000000000110001c000200;WGT=1;dbSNPBuildID=137
chr1 8714 rs199948150 GC G . PASS OTHERKG;RS=199948150;RSPOS=233686;SAO=0;SSR=0;VC=DIV;VP=0x050000000001000002000200;WGT=1;dbSNPBuildID=137
chr1 9261 rs201432159 G A . PASS OTHERKG;RS=201432159;RSPOS=234232;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000002000100;WGT=1;dbSNPBuildID=137
chr1 9342 rs56055731 C T . PASS HD;OTHERKG;RS=56055731;RSPOS=234313;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000402000100;WGT=1;dbSNPBuildID=129
chr1 9435 rs111659307 A G . PASS OTHERKG;RS=111659307;RSPOS=234408;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000002000100;WGT=1;dbSNPBuildID=132
chr1 9508 rs8179403 T A . PASS GNO;OTHERKG;RS=8179403;RSPOS=234481;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=0x050100000001040102000100;WGT=1;dbSNPBuildID=117
chr1 9558 rs111281142 A G . PASS OTHERKG;RS=111281142;RSPOS=234534;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000002000100;WGT=1;dbSNPBuildID=132
chr1 9580 rs113278145 C T . PASS OTHERKG;RS=113278145;RSPOS=234556;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000002000100;WGT=1;dbSNPBuildID=132One note worthy thing is that I am actually testing CHM13 for somatic variant calling and am trying to at least do BQSR, so I lifted the Homo_Sapiens_Assembly38.vcf with CrossMap using a chain file then splitted the lines that includes "duplicated alleles" such as (REF:G, ALT:G,A to REF:G, ALT:G and REF:G ALT:A) then removed the lines where there are only G (REF:G, ALT:G).
I would really, really appreciate any help. Thanks!!
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Hi Heather Peng
Looks like your file is lacking a proper header section for a VCF therefore our tool cannot index.
Regards.
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Gökalp Çelik Thank you so much I'll look into that right now.
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After a series of revising, I got A USER ERROR has occurred: Error while trying to create index for sorted_filtered_knownsites.vcf. Error was: htsjdk.tribble.TribbleException: Line 94: there aren't enough columns for line (we expected 9 tokens, and saw 1 )
when I sed -n '94p' sorted_filtered_knownsites.vcf, I got
#CHROM POS ID REF ALT QUAL FILTER INFO
what could be the problem? Thank you! -
Those columns must be tab separated. If not it will only detect one column.
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Thank you for your fast response!
However when `cat -A sorted_filtered_knownsites.vcf | sed -n '94p'`, it did gave me #CHROM^IPOS^IID^IREF^IALT^IQUAL^IFILTER^IINFO$ so I guess it's tab separated already?
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You may need to run ValidateVariants tool to check the integrity of the VCF file.
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I ran it but it is still returning
tsjdk.tribble.TribbleException: Line 94: there aren't enough columns for line (we expected 9 tokens, and saw 1 ), for input source: sorted_filtered_knownsites.vcfSorry to keep asking but is there any other angle I could look into this issue?
Thank you!
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Your VCF is malformed at line 94. There is certainly an incompatible separator for the line that is in effect. Tab separator is '\t' therefore you need to fix that line with the proper separator. Without this fix there is really no way to continue further from this point.
Regards.
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I tried all the ways I could think of, still getting the same error.. so I tried to compare the two:
cat -A Homo_sapiens_assembly38.vcf | sed -n '3436p'
#CHROM^IPOS^IID^IREF^IALT^IQUAL^IFILTER^IINFO$cat -A v2_tabbed_knownsites.vcf | sed -n '94p'
#CHROM^IPOS^IID^IREF^IALT^IQUAL^IFILTER^IINFO$They are giving same results, is this the end of this road?
Thank you for your patience. -
If there is a way that you can open this file with a text editor you may be able to see if those columns are separated with tab or not. Commandline does not always show those whitespace characters correctly.
You can grab the header section of the file with
bcftools view -h
and later fix the corresponding line and later reheader the file with bcftools reheader tool to see if it works. If you are not satisfied with GATK's error message you may be able to try bgzipping and indexing the file with bgzip and tabix to see if they also raise an error with that file.
I hope these help.
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Can you also check the 94th variant entry in the file below the header section?
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Just a tiny addition to Gökalp Çelik's suggestions regarding potential whitespace issues; the last two replies on this thread might be worth checking out:
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Gökalp Çelik Can Kockan Thank you for kindly advising the next step.
I think something went wrong at the very start (i.e. CrossMap) so decided to take alternative route to approach CHM13 somatic calling.
Still the above discuss helped me gain a lot of insights into VCF procssing, much appreciated!!
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