Having issues with combine_vcf.py

[ilariastewart]

Hi there,
I ran the newest vamos on my cohort and trying to merge the vcf files. I am running into issues with the combine_vcf.py script. I had to make a change to the script to initialize the sample variable and now am getting issues with the readOneVCF function:

python3 combine_vcf.py -i vamos_calls.csv -o vamos_merged_output.vcf
2023-12-11 10:45:34 - INFO - Parsing Input Arguements...
2023-12-11 10:45:34 - INFO - Required Argument - inVCFs: vamos_calls.csv
2023-12-11 10:45:34 - INFO - Required Argument - outVCF: vamos_merged_output.vcf
2023-12-11 10:45:34 - INFO - Parsing Input Arguements Completed

Traceback (most recent call last):
  File "/mnt/scratch/ilaria/VNTR/vamos_sherlock/ADRC_vamos/combine_vcf.py", line 197, in <module>
    samplesAll, header, vcfDict = readAllVCF(inVCFs)
                                  ^^^^^^^^^^^^^^^^^^
  File "/mnt/scratch/ilaria/VNTR/vamos_sherlock/ADRC_vamos/combine_vcf.py", line 160, in readAllVCF
    readOneVCF(vcfs[0],vcfDict)
  File "/mnt/scratch/ilaria/VNTR/vamos_sherlock/ADRC_vamos/combine_vcf.py", line 90, in readOneVCF
    coor, constant, altannoH1, altannoH2 = readOneVCFLine(line,vcfDict)
                                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/scratch/ilaria/VNTR/vamos_sherlock/ADRC_vamos/combine_vcf.py", line 61, in readOneVCFLine
    chr,pos,id,ref,alt,qual,filter,info,_,_ = line.strip().split('\t')
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: not enough values to unpack (expected 10, got 3)

Thank you for any insights you can provide!

[BidaGu]

Hi Ilaria,

Based on the error massage, it seems that the program parsed a strange entry that has only 3 fields as a Tandem Repeat entry line (which should have 10 fields) in the vcf.

The script was written to parse the "sample" (i.e., the sample name of each input vcf) variable directly from input vcfs. The sample name taken from each individual vcf is the last field of the last header line of each vcf. Was there an issue if you run the script without modifying it?

Thanks,
Bida

[ilariastewart]

Hi Bida, Thanks for your quick response! When running the unedited version I get this: python3 combine_vcf_original.py -i vamos_calls.csv -o merged_output.vcf 2023-12-11 16:44:21 - INFO - Parsing Input Arguements... 2023-12-11 16:44:21 - INFO - Required Argument - inVCFs: vamos_calls.csv 2023-12-11 16:44:21 - INFO - Required Argument - outVCF: merged_output.vcf 2023-12-11 16:44:21 - INFO - Parsing Input Arguements Completed Traceback (most recent call last): File "/mnt/scratch/ilaria/VNTR/vamos_sherlock/ADRC_vamos/combine_vcf_original.py", line 193, in <module> samplesAll, header, vcfDict = readAllVCF(inVCFs) ^^^^^^^^^^^^^^^^^^ File "/mnt/scratch/ilaria/VNTR/vamos_sherlock/ADRC_vamos/combine_vcf_original.py", line 138, in readAllVCF samplesAll.append(getVCFSampleName(vcfs[0])) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/mnt/scratch/ilaria/VNTR/vamos_sherlock/ADRC_vamos/combine_vcf_original.py", line 52, in getVCFSampleName return sample ^^^^^^ UnboundLocalError: cannot access local variable 'sample' where it is not associated with a value Thanks, Ilaria From: Bida Gu ***@***.***> Date: Monday, December 11, 2023 at 3:53 PM To: ChaissonLab/vamos ***@***.***> Cc: Ilaria Stewart ***@***.***>, Author ***@***.***> Subject: Re: [ChaissonLab/vamos] Having issues with combine_vcf.py (Issue #5) Hi Ilaria, Based on the error massage, it seems that the program parsed a strange entry that has only 3 fields as a Tandem Repeat entry line (which should have 10 fields) in the vcf. The script was written to parse the "sample" (i.e., the sample name of each input vcf) variable directly from input vcfs. The sample name taken from each individual vcf is the last field of the last header line of each vcf. Was there an issue if you run the script without modifying it? Thanks, Bida — Reply to this email directly, view it on GitHub<#5 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BDLIGF7S5YS2RVQ3VOWKY4DYI6MF5AVCNFSM6AAAAABAQHTMH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJRGA4DAOBRGE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[BidaGu]

Hi Ilaria,

Could you please also share the command you used to run vamos? Thanks!

[ilariastewart]

Hi Bida, Certainly! Here is what I ran to iterate through our cohort: set -x # Print the activation command echo "Activating Vamos environment:" source activate vamos # Run Vamos command # Specify the Vamos parameters VAMOS_COMMAND="vamos --read -b" VAMOS_REGION="-r /home/users/ilaria99/vntr_region_motifs.e.bed" OUTPUT_DIR="/scratch/users/ilaria99" THREADS=4 # Directory containing subject directories SUBJECT_DIR="/oak/output" # Iterate through each subject directory for dir in "$SUBJECT_DIR"/*; do if [ -d "$dir" ]; then dir_name=$(basename "$dir") input_bam="$SUBJECT_DIR/$dir_name/$dir_name.GRCh38.sorted.bam" output_vcf="$OUTPUT_DIR/${dir_name}_vamos_reads.vcf" # Check if the output VCF file already exists if [ -e "$output_vcf" ]; then echo "Skipping $input_bam - VCF file already exists: $output_vcf" else # Run Vamos on the BAM file echo "Running Vamos on $input_bam" $VAMOS_COMMAND "$input_bam" $VAMOS_REGION -s "$dir_name" -o "$output_vcf" -t "$THREADS" fi fi done Best, Ilaria From: Bida Gu ***@***.***> Date: Monday, December 11, 2023 at 5:37 PM To: ChaissonLab/vamos ***@***.***> Cc: Ilaria Stewart ***@***.***>, Author ***@***.***> Subject: Re: [ChaissonLab/vamos] Having issues with combine_vcf.py (Issue #5) Hi Ilaria, Could you please also share the command you used to run vamos? Thanks! — Reply to this email directly, view it on GitHub<#5 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BDLIGF7CGZCESAYWBYBQTL3YI6YOLAVCNFSM6AAAAABAQHTMH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJRGE3DKNZRG4>. You are receiving this because you authored the thread.Message ID: ***@***.***>