robertwhbaldwin

Sorry I deleted the square.vcf I only have the square.anno.vcf. Below are some records from that file. If you have genotypes in the anno file and the header lists 25...

yes truncated the final record in squared.vcf was incomplete . thanks for your help - Robert

o.k thanks for clarifying. I ran the genotype command while looping over my samples so should have used the exact same command. it's too late now to check whether they...

Even when I run this command: for i in `cat baselist`; do smoove genotype -d -x -p 10 --name ${i}-joint --outdir /data/results --fasta /assembly/GCF_014851395.1_ASM1485139v1_genomic.fa --vcf /data/merged.sites.vcf.gz /data/${i}.bam; done for all...

I'm also seeing these errors during joint calling: [smoove] 2021/08/03 15:16:50 [W::vcf_parse_format] FORMAT 'A4462e-05,9.99482e-06,9.56203e-06,9.14399e-06,8.74227e-06,8.35393e-06,7.98703e-06,7.61705e-06,7.27361e-06,6.94555e-06,6.62552e-06,6.32885e-06,6.04414e-06,5.77125e-06,5.51789e-06,5.25973e-06,5.0192e-06,4.79523e-06,4.57402e-06,4.36612e-06,4.16652e-06,3.96759e-06,3.78389e-06,3.6099e-06,3.44453e-06,3.28004e-06,3.12227e-06,2.97154e-06,2.82559e-06,2.69954e-06,2.57222e-06,2.44853e-06,2.33466e-06,2.2263e-06,2.12208e-06,2.01915e-06,1.92205e-06,1.82788e-06,1.74149e-06,1.66091e-06,1.58236e-06,1.50756e-06,1.43164e-06,1.363e-06,1.29843e-06,1.23655e-06,1.17697e-06,1.11952e-06,1.0653e-06,1.01308e-06,9.63941e-07,9.17687e-07,8.74143e-07,8.31384e-07,7.91683e-07,7.51918e-07,7.14817e-07,6.79541e-07,6.4406e-07,6.12144e-07,5.82663e-07,5.54434e-07,5.28663e-07,5.03053e-07,4.79452e-07,4.55018e-07,4.32446e-07,4.09692e-07,3.88321e-07,3.68644e-07,3.49889e-07,3.32023e-07,3.15341e-07,2.99866e-07,2.8467e-07,2.70208e-07,2.56401e-07,2.43247e-07,2.30699e-07,2.18665e-07,2.07311e-07,1.96745e-07,1.86553e-07,1.77256e-07,1.68018e-07,1.59288e-07,1.51459e-07,1.43329e-07,1.35834e-07,1.28571e-07,1.21877e-07,1.15675e-07,1.09439e-07,1.04061e-07,9.8893e-08,9.37313e-08,8.90025e-08,8.43316e-08,7.96874e-08,7.51901e-08,7.12716e-08,6.76328e-08,6.39367e-08,6.04708e-08,5.71726e-08,5.42114e-08,5.13109e-08,4.85794e-08,4.5978e-08,4.35303e-08,4.09953e-08,3.87095e-08,3.64666e-08,3.44176e-08,3.25053e-08,3.06859e-08,2.90966e-08,2.743e-08,2.58987e-08,2.44369e-08,2.30967e-08,2.17873e-08,2.05329e-08,1.93676e-08,1.8296e-08,1.72166e-08,1.6234e-08,1.52826e-08,1.4375e-08,1.35486e-08,1.27192e-08,1.193e-08,1.12165e-08,1.05456e-08,9.97098e-09,9.43084e-09,8.91486e-09,8.44277e-09,7.9977e-09,7.55771e-09,7.13893e-09,6.71683e-09,6.33154e-09,5.96088e-09,5.61822e-09,5.29998e-09,4.99889e-09,4.71517e-09,4.43637e-09,4.19144e-09,3.9445e-09,3.71646e-09,3.49714e-09,3.2917e-09,3.11296e-09,2.92939e-09,2.76526e-09,2.60389e-09,2.44918e-09,2.31001e-09,2.1729e-09,2.04672e-09,1.92188e-09,1.80769e-09,1.70431e-09,1.60108e-09,1.50772e-09,1.42006e-09,1.33768e-09,1.25527e-09,1.17883e-09,1.10978e-09,1.04238e-09,9.75512e-10,9.1928e-10,8.61022e-10,8.06906e-10,7.57484e-10,7.1298e-10,6.68795e-10,6.2694e-10,5.88943e-10,5.53005e-10,5.19354e-10,4.8772e-10,4.57694e-10,4.30622e-10,4.04646e-10,3.79352e-10,3.5691e-10,3.33495e-10,3.12482e-10,2.92991e-10,2.73781e-10,2.56513e-10,2.40926e-10,2.25187e-10,2.10308e-10,1.97384e-10,1.84986e-10,1.72565e-10,1.62108e-10,1.51541e-10,1.42223e-10,1.33086e-10,1.24448e-10,1.15557e-10,1.07781e-10,1.01272e-10,9.46485e-11,8.85283e-11,8.26293e-11,7.72608e-11,7.23201e-11,6.7415e-11,6.28031e-11,5.84444e-11,5.45829e-11,5.09556e-11,4.75788e-11,4.44747e-11,4.15533e-11,3.87346e-11,3.61179e-11,3.37852e-11,3.14856e-11,2.94408e-11,2.75161e-11,2.56805e-11,2.39672e-11,2.23002e-11,2.08202e-11,1.93707e-11,1.80671e-11,1.67861e-11,1.55708e-11,1.44695e-11,1.34059e-11,1.24725e-11,1.16153e-11,1.07633e-11,1.00117e-11,9.33656e-12,8.66087e-12,8.05219e-12,7.51755e-12,6.98282e-12,6.5046e-12,6.06261e-12,5.64797e-12,5.28458e-12,4.91142e-12,4.59546e-12,4.27418e-12,3.98484e-12,3.71151e-12,3.44513e-12,3.20027e-12,2.98023e-12,2.77695e-12,2.57018e-12,2.38511e-12,2.22187e-12,2.07088e-12,1.92366e-12,1.79105e-12,1.65832e-12,1.52947e-12,1.41877e-12,1.30576e-12,1.21241e-12,1.12738e-12,1.04927e-12,9.7001e-13,8.97196e-13,8.28728e-13,7.65882e-13,7.07849e-13,6.53627e-13,6.07382e-13,5.63034e-13,5.20092e-13,4.83506e-13,4.47687e-13,4.14958e-13,3.79208e-13,3.52904e-13,3.24956e-13,2.98167e-13,2.75161e-13,2.54071e-13,2.35399e-13,2.19121e-13,2.01519e-13,1.87135e-13,1.73503e-13,1.59428e-13,1.46991e-13,1.35424e-13,1.24415e-13,1.15594e-13,1.06617e-13,9.83493e-14,9.0559e-14,8.32674e-14,7.71632e-14,7.05748e-14,6.54735e-14,6.0747e-14,5.59402e-14,5.14873e-14,4.74987e-14,4.36525e-14,4.03392e-14,3.72438e-14,3.43118e-14,3.16196e-14,2.89851e-14,2.66163e-14,2.45617e-14,2.24962e-14,2.07907e-14,1.9218e-14,1.76712e-14,1.6313e-14,1.51126e-14,1.39533e-14,1.27723e-14,1.17356e-14,1.08444e-14,9.90892e-15,9.08689e-15,8.37971e-15,7.71313e-15,7.06398e-15,6.51524e-15,5.99773e-15,5.52297e-15;AC=1;AN=2;SNAME=RHF05342' at NW_024042261.1:3152646 is not defined in the header, assuming Type=String [smoove] 2021/08/03 15:16:50 [E::bcf_hdr_parse_line] Could not...

I don't see how that's possible. I restart the computer and start a new job and delete the old files and still get these messages. I can try running with...

I grabbed the RG from the header of the bams for each sample like this: for i in `cat baselist`; do samtools view -H ${i}.bam | grep "^@RG" >RG_${i}; done...

I got genotyping to work it in a single command, no prend warnings and the exact same number of variants per file. All I did was move the data from...

The first step in population calling I used this: smoove call --outdir results-smoove/ --name $sample --fasta $reference_fasta -p 1 --genotype /path/to/$sample.bam Basically, what you stated on in the doc but...

yes, there's a problem with the samples with no vcf from the call step, a lot of overlapping reads, for example. I ran picard collect_wgs_metrics and after you exclude overlapping...