On Mon, 16 Apr 2018, RITSUKO OIKAWA wrote:
Samtools does have an option to *filter* the reads according to regions
specified in the BED format.
$ samtools view -hL chr22_21804028_ref.Gene.bed PLCPRF5bis44.sam >
PLCPRF5bis44.filtered.sam
[E::sam_parse1] missing SAM header
[W::sam_read1] Parse e
Hi,
HTSLIB 1.5 and 1.8 both have a bug in tabix. It ignores the option for
0-based input files.
Example: I have a vcf with two consecutive variants
chr22 17491115 . C T 1189.33 PASS [...]
chr22 17491116 . G A 16942.9 PASS [...]
I have a bed file requesting these 2 entries:
chr22 17491114 174911
Hi,
I am using tabix -R to do multiple-chromosome extraction from a sorted and
indexed annotation file given a bed file with all indexes that need to be
filtered. The command is 'tabix annotationfile.bgz -R bedfile.bed'. The bed
file looks like:
1 1157280 1157281
2 53893683 53893684
...
But I
