Hello.
I am just seeing if this method for VCF creating for variant calls is correct.
Right now I keep the fastq as an entire file, and then align the whole fastq file to individual chromosomes, and this produces a VCF file for each chromosome that I later merge together.
However this can cause errors if the alignment has a poor map to the individual chromosome because it will generate a forced alignment, even if it maps poorly to the chromosome. (ie the VCF call will show a score to the poor map of the fastq to the chromosome if there is only a single chromosome the fastq is being aligned to:: (ie. reducing the domain of the fastq to a single chromsome at a time)
Is it better not to reduce the alignment map to a single chromosome at a time and instead map to the whole chromosome at once?
I am just seeing if this method for VCF creating for variant calls is correct.
Right now I keep the fastq as an entire file, and then align the whole fastq file to individual chromosomes, and this produces a VCF file for each chromosome that I later merge together.
However this can cause errors if the alignment has a poor map to the individual chromosome because it will generate a forced alignment, even if it maps poorly to the chromosome. (ie the VCF call will show a score to the poor map of the fastq to the chromosome if there is only a single chromosome the fastq is being aligned to:: (ie. reducing the domain of the fastq to a single chromsome at a time)
Is it better not to reduce the alignment map to a single chromosome at a time and instead map to the whole chromosome at once?
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