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File format are sets of defined rules to organise a specific type of data. Common file format in bioinformatics include FASTA, FASTQ, SAM, BAM, VCF.

7
votes
This is an early Solexa/Illumina sequencer format. The columns are the identifier to location on the flowcell. I believe the "." was the original placeholder for an unread base, which has been replac …
answered Oct 31 '17 by Bioathlete
0
votes
As far as I know you can not write compressed fastq on the fly. You will have to write the entire fastq and then compress it.
answered Jun 24 '17 by Bioathlete
2
votes
Yes the compressed outputs should be the same format as bgzip. bcftools also has an option to index in either the CSI or TBI formats. The index function mentions that it indexes bgzip compressed fil …
answered Nov 20 '17 by Bioathlete
2
votes
The filtering criteria should be defined in the header of the VCF file. Can you include the header from your VCF file? VCF Format and example header: FILTERs that have been applied to the data shou …
answered Jun 27 '18 by Bioathlete