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Update CollectSamErrorMetrics.java #1340

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Update CollectSamErrorMetrics.java #1340

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Update CollectSamErrorMetrics.java
nh13 Jun 3, 2019
ca9d000
Update CollectSamErrorMetrics.java
nh13 Jun 3, 2019
12f2e9b
Resolve merge conflicts
kockan Feb 15, 2024
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2 changes: 1 addition & 1 deletion src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java
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Expand Up @@ -167,7 +167,7 @@ public class CollectSamErrorMetrics extends CommandLineProgram {
public ReadBaseStratification.Stratifier STRATIFIER_VALUE;

@Argument(shortName = "V", doc = "VCF of known variation for sample. program will skip over polymorphic sites in this VCF and " +
"avoid collecting data on these loci.")
"avoid collecting data on these loci.", optional = true)
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hmmm. Collecting error metrics over variants doesn't make much sense...you could give it dbSNP or something like that if you dont' have truth for that sample....

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What if my sample has no variants relative the reference? That’s my real use case! No VCF is required. Think sequencing bacteria or synthetic sequences.

public String VCF;

@Argument(shortName = "L", doc = "Region(s) to limit analysis to. Supported formats are VCF or interval_list. Will *intersect* inputs if multiple are given. " +
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