If I use a sampleNames_file do the BAM files need to specify SM= in the header ?

[Boo Guy]

HI 

If I use  a sampleNames_file do the BAM files need  to specify  SM= in the header ?

Currently my indexed .bam files have not SM= specified.

Currently I am getting the following error and cannot figure it out.

Program start [2021-03-01 22:24:29] Get and validate pos and gen Error in names(x) <- value : 'names' attribute [4] must be the same length as the vector [1] 

any ideas?

Thanks 

Guy

I am uses the latest version of STITCH, the test datasets works for me.

head of bamlist 

/home/reeves/oldbamtest/bams/GuysOldBam/b106_10.bam

/home/reeves/oldbamtest/bams/GuysOldBam/b106_19.bam

/home/reeves/oldbamtest/bams/GuysOldBam/b106_30.bam

head of sampleNames_file

b106_10

b106_19

b106_30

[2021-03-01 22:24:29] Running STITCH(chr = chr2L, nGen = 11, posfile = posfileREF.txt, K = 4, S = 1, outputdir = /home/reeves/oldbamtest/, nStarts = , tempdir = /tmp/Rtmpflbp7l, bamlist = listOfFiles_GuysOldBam.txt, cramlist = , sampleNames_file = names_GuysOldBam.txt, reference = , genfile = , method = diploid, output_format = bgvcf, B_bit_prob = 16, outputInputInVCFFormat = TRUE, downsampleToCov = 50, downsampleFraction = 1, readAware = TRUE, chrStart = NA, chrEnd = NA, regionStart = NA, regionEnd = NA, buffer = NA, maxDifferenceBetweenReads = 1000, maxEmissionMatrixDifference = 10000000000, alphaMatThreshold = 0.0001, emissionThreshold = 0.0001, iSizeUpperLimit = 600, bqFilter = 17, niterations = 40, shuffleHaplotypeIterations = c(4, 8, 12, 16), splitReadIterations = 25, nCores = 12, expRate = 0.5, maxRate = 100, minRate = 0.1, Jmax = 1000, regenerateInput = TRUE, originalRegionName = NA, keepInterimFiles = FALSE, keepTempDir = FALSE, outputHaplotypeProbabilities = FALSE, switchModelIteration = NA, generateInputOnly = FALSE, restartIterations = NA, refillIterations = c(6, 10, 14, 18), downsampleSamples = 1, downsampleSamplesKeepList = NA, subsetSNPsfile = NA, useSoftClippedBases = FALSE, outputBlockSize = 1000, outputSNPBlockSize = 10000, inputBundleBlockSize = NA, genetic_map_file = , reference_haplotype_file = , reference_legend_file = , reference_sample_file = , reference_populations = NA, reference_phred = 20, reference_iterations = 40, reference_shuffleHaplotypeIterations = c(4, 8, 12, 16), output_filename = NULL, initial_min_hapProb = 0.2, initial_max_hapProb = 0.8, regenerateInputWithDefaultValues = FALSE, plotHapSumDuringIterations = FALSE, plot_shuffle_haplotype_attempts = FALSE, plotAfterImputation = TRUE, save_sampleReadsInfo = FALSE, gridWindowSize = NA, shuffle_bin_nSNPs = NULL, shuffle_bin_radius = 5000, keepSampleReadsInRAM = FALSE, useTempdirWhileWriting = FALSE, output_haplotype_dosages = FALSE, use_bx_tag = TRUE, bxTagUpperLimit = 50000) [2021-03-01 22:24:29] Program start [2021-03-01 22:24:29] Get and validate pos and gen Error in names(x) <- value : 'names' attribute [4] must be the same length as the vector [1]

[Robbie Davies]

Hi Guy,

You should be able to use sampleNames_file to avoid specifying SM= in the header. I just tried and it's working for me.

The error message suggests the posfile is malformed? Could you check that it's tab separated and otherwise matches the format of the test data?

Best,

Robbie

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[Boo Guy]

Dear Robbie 

It was not tabbed as you suspected.  Once I also removed the all the indels so only SNPs were present it started to run.

Thanks 

Guy